MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'SAR and QSAR in Environmental Research' source. Thu, 09 Feb 2012 11:36:08 +0100 http://www.medworm.com/index.php?rid=5594577&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22224473%26dopt%3DAbstract In this study, the depuration half-lives of 62 polychlorinated biphenyl (PCB) congeners in juvenile rainbow trout (Oncorhynchus mykiss) were estimated from their structural features based on QSPR methodology. A genetic algorithm (GA) was applied as a variable subset selection strategy and QSPR models established upon multiple linear regression (MLR), multilayer perceptron neural network (MLP NN) and support vector regression (SVR) procedures. Robustness and predictive stability of the constructed models were evaluated through internal and external validation methods. The high numerical values of [Formula: see text] and [Formula: see text], and low RMSE in the case of the MLP NN model, confirm the supremacy of this model as well as nonlinear dependency of molecular structural features to th... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5594577 Mon, 09 Jan 2012 05:00:00 +0100 5594577 http://www.medworm.com/index.php?rid=5594576&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22224501%26dopt%3DAbstract Authors: Cao DS, Zhao JC, Yang YN, Zhao CX, Yan J, Liu S, Hu QN, Xu QS, Liang YZ Abstract There is a great need to assess the harmful effects or toxicities of chemicals to which man is exposed. In the present paper, the simplified molecular input line entry specification (SMILES) representation-based string kernel, together with the state-of-the-art support vector machine (SVM) algorithm, were used to classify the toxicity of chemicals from the US Environmental Protection Agency Distributed Structure-Searchable Toxicity (DSSTox) database network. In this method, the molecular structure can be directly encoded by a series of SMILES substrings that represent the presence of some chemical elements and different kinds of chemical bonds (double, triple and stereochemistry) in the molecu... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5594576 Mon, 09 Jan 2012 05:00:00 +0100 5594576 http://www.medworm.com/index.php?rid=5504886&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22150015%26dopt%3DAbstract Authors: Furuhama A, Aoki Y, Shiraishi H Abstract To understand the key factor for fish toxicity of 11 α,β-unsaturated carbonyl aldehydes and ketones, we used quantum chemical calculations to investigate their Michael reactions with methanethiol or glutathione. We used two reaction schemes, with and without an explicit water molecule (Scheme-1wat and Scheme-0wat, respectively), to account for the effects of a catalytic water molecule on the reaction pathway. We determined the energies of the reactants, transition states (TS), and products, as well as the activation energies of the reactions. The acute fish toxicities of nine of the carbonyl compounds were evaluated to correlate with their hydrophobicities; no correlation was observed for acrolein and crotonaldehyde. The most toxi... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5504886 Thu, 08 Dec 2011 05:00:00 +0100 5504886 http://www.medworm.com/index.php?rid=5504885&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22150068%26dopt%3DAbstract Authors: Wen Y, Su LM, Qin WC, He J, Fu L, Zhang XJ, Zhao YH Abstract The relationship between log K (oc) and log P was examined by use of a large dataset. For most of the hydrophobic compounds (e.g. 0.5 < log P < 7.5), the organic carbon content plays a dominant role in soil sorption and the sorption coefficient is linearly related to the octanol/water partition coefficient. For hydrophilic compounds (e.g. log P < 0.5), hydrophobic sorption becomes less significant. The hydrophilic contribution to sorption is equal to, or higher than, the hydrophobic contribution to sorption, resulting in the observed K (oc) values being higher than those predicted from their log P values. For highly hydrophobic compounds (e.g. log P > 7.5), log K (oc) decreases with in... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5504885 Thu, 08 Dec 2011 05:00:00 +0100 5504885 http://www.medworm.com/index.php?rid=5504884&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22150106%26dopt%3DAbstract Authors: Gonzalez J, Marchand-Geneste N, Giraudel JL, Shimada T Abstract To obtain chemical clues on the process of bioactivation by cytochromes P450 1A1 and 1B1, some QSAR studies were carried out based on cellular experiments of the metabolic activation of polycyclic aromatic hydrocarbons and heterocyclic aromatic compounds by those enzymes. Firstly, the 3D structures of cytochromes 1A1 and 1B1 were built using homology modelling with a cytochrome 1A2 template. Using these structures, 32 ligands including heterocyclic aromatic compounds, polycyclic aromatic hydrocarbons and corresponding diols, were docked with LigandFit and CDOCKER algorithms. Binding mode analysis highlighted the importance of hydrophobic interactions and the hydrogen bonding network between cytochrome amino ac... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5504884 Thu, 08 Dec 2011 05:00:00 +0100 5504884 http://www.medworm.com/index.php?rid=5375259&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22040297%26dopt%3DAbstract Authors: Bagheri M, Golbraikh A Abstract The solubility parameter (δ) plays a unique role in the development of stable pharmaceutical formulations for assessing phase segregation during product synthesis. Understanding this parameter helps to determine how a drug substance will behave when processed or when dosed in vivo. The aim of this work was to develop a novel comprehensive yet rapid and accurate Quantitative Structure-Property Relationship (QSPR) method based on the rank-based ant system feature selection. The method was coupled with the multiple linear regression and support vector regression and applied to the assessment of solubility parameters for a diverse dataset of 1804 chemical compounds. The models were validated by solubility prediction of 360 test set compounds w... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5375259 Mon, 31 Oct 2011 04:00:00 +0100 5375259 http://www.medworm.com/index.php?rid=5375258&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22040327%26dopt%3DAbstract Authors: Abbasitabar F, Zare-Shahabadi V Abstract Quantitative structure-activity relationship (QSAR) models were derived for 179 analogues of artemisinin, a potent antimalarial agent. The activities of these compounds were investigated by means of multiple linear regression (MLR). To select relevant descriptors, several methods including stepwise selection, successive projection algorithm and an ant colony optimization algorithm (called memorized_ACS) were employed. A wide variety of molecular descriptors belonging to various structural properties were calculated for each molecule. Two matrixes (D1 and D2) of molecular properties were built. The D1 matrix included the calculated descriptors and the D2 matrix contained the first to third orders of the calculated descriptors and the... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5375258 Mon, 31 Oct 2011 04:00:00 +0100 5375258 http://www.medworm.com/index.php?rid=5339535&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22014213%26dopt%3DAbstract Authors: Mombelli E Abstract The determination of binding affinities for the estrogen receptor (ER) is used extensively to assess potential hazards to human health and the environment arising from chemicals that can interfere with natural hormone homeostasis. Given the great number of chemicals to which humans and wildlife are exposed, (quantitative) structure-activity relationship (Q)SAR models for the characterization of ER disruptors represent a fast and cost-efficient alternative to experimental testing. In this toxicological context, the freely available Organisation for Economic Co-operation and Development (OECD) (Q)SAR Application Toolbox provides a profiler for the categorical profiling of chemicals according to their ER binding propensities. The aim of this study was to e... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5339535 Fri, 21 Oct 2011 04:00:00 +0100 5339535 http://www.medworm.com/index.php?rid=5339534&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22014234%26dopt%3DAbstract Authors: Dimitrov S, Dimitrova N, Georgieva D, Vasilev K, Hatfield T, Straka J, Mekenyan O Abstract The new development of the bioconcentration factor (BCF) base-line model of Dimitrov et al. [SAR QSAR Environ. Res. 6 (2005), pp. 531-554] is presented. The model applicability domain was expanded by enlarging the training set of the model up to 705 chemicals. The list of chemical-dependent mitigating factors was expanded by including water solubility of chemicals. The original empirical term for estimating ionization of chemicals was mechanistically analysed using two different approaches. In the first one, the ionization potential of chemicals was estimated based on the acid dissociation constant (pK(a) ). This term was found to be less adequate for inclusion in the ultimate BCF m... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5339534 Fri, 21 Oct 2011 04:00:00 +0100 5339534 http://www.medworm.com/index.php?rid=5339538&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22003826%26dopt%3DAbstract Authors: Luilo GB, Cabaniss SE Abstract Chlorinating water which contains dissolved organic matter (DOM) produces disinfection byproducts, the majority of unknown structure. Hence, the total organic halide (TOX) measurement is used as a surrogate for toxic disinfection byproducts. This work derives a robust quantitative structure-property relationship (QSPR) for predicting the TOX formation potential of model compounds. Literature data for 49 compounds were used to train the QSPR in moles of chlorine per mole of compound (Cp) (mol-Cl/mol-Cp). The resulting QSPR has four descriptors, calibration [Formula: see text] of 0.72 and standard deviation of estimation of 0.43 mol-Cl/mol-Cp. Internal and external validation indicate that the QSPR has good predictive power and low bias (‰&l... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5339538 Tue, 18 Oct 2011 04:00:00 +0100 5339538 http://www.medworm.com/index.php?rid=5339537&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004550%26dopt%3DAbstract Authors: Sridhar J, Foroozesh M, Stevens CL Abstract Quantitative structure-activity relationship (QSAR) studies were conducted on an in-house database of cytochrome P450 enzyme 1A2 inhibitors using the comparative molecular field analysis (CoMFA), comparative molecular similarity analysis (CoMSIA) and hologram QSAR (HQSAR) approaches. The database consisted of 36 active molecules featuring varied core structures. The model based on the naphthalene substructure alignment incorporating 19 molecules yielded the best model with a CoMFA cross validation value q(2) of 0.667 and a Pearson correlation coefficient r(2) of 0.976; a CoMSIA q(2) value of 0.616 and r(2) value of 0.985; and a HQSAR q(2) value of 0.652 and r(2) value of 0.917. A second model incorporating 34 molecules aligned us... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5339537 Mon, 17 Oct 2011 04:00:00 +0100 5339537 http://www.medworm.com/index.php?rid=5339536&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22004567%26dopt%3DAbstract Authors: Wang JH, Hou QQ, Tang K, Cheng XL, Dong LH, Liu YJ, Liu CB Abstract Receptor-based comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on a series of 54 progesterone receptor (PR) inhibitors. The established CoMFA model from the training set gives statistically significant results with the cross-validated q (2) of 0.534 and non-cross-validated [Formula: see text] of 0.947. The best CoMSIA model was derived by the combination of steric field and hydrophobic field with a q (2) of 0.615 and [Formula: see text] of 0.954. A test set of 18 compounds was used to validate the predictive ability of the two models. The predicted correlation coefficients [Formula: see text] are 0.681 and 0.677 for CoMFA and CoMSIA... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5339536 Mon, 17 Oct 2011 04:00:00 +0100 5339536 http://www.medworm.com/index.php?rid=5339543&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21999104%26dopt%3DAbstract Authors: Dimitrov S, Pavlov T, Veith G, Mekenyan O Abstract Information regarding the metabolism of xenobiotic chemicals plays a central role in regulatory risk assessments. In regulatory programmes where metabolism studies are required, the studies of metabolic pathways are often incomplete and the identification of activated metabolites and important degradation products are limited by analytical methods. Because so many more new chemicals are being produced than can be assessed for potential hazards, setting assessment priorities among the thousands of untested chemicals requires methods for predictive hazard identification which can be derived directly from chemical structure and their likely metabolites. In a series of papers we are sharing our experience in the computerized m... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5339543 Fri, 14 Oct 2011 04:00:00 +0100 5339543 http://www.medworm.com/index.php?rid=5339542&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21999713%26dopt%3DAbstract Authors: Carbó-Dorca R, Besalú E Abstract The structure one can associate to coherent nano-quantitative structure-properties relationship (nano-QSPR) models is briefly discussed. Such nano-QSPR model functions are described as possessing three parts: a particle size polynomial; a typical QSPR function; and a special effects function. The expected behaviour of the particle size part is discussed from the point of view of catastrophe theory, in this way providing a plausible general picture about the emergence of new properties of nanoparticles and holographic location of information content. PMID: 21999713 [PubMed - as supplied by publisher] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5339542 Fri, 14 Oct 2011 04:00:00 +0100 5339542 http://www.medworm.com/index.php?rid=5339541&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21999753%26dopt%3DAbstract Authors: Moosus M, Maran U Abstract Quantitative structure-activity relationship analysis and estimation of toxicological effects at lower-mid trophic levels provide first aid means to understand the toxicity of chemicals. Daphnia magna serves as a good starting point for such toxicity studies and is also recognized for regulatory use in estimating the risk of chemicals. The ECOTOX database was queried and analysed for available data and a homogenous subset of 253 compounds for the endpoint LC50 48 h was established. A four-parameter quantitative structure-activity relationship was derived (coefficient of determination, r (2) = 0.740) for half of the compounds and internally validated (leave-one-out cross-validated coefficient of determination, [Formula: see text] = 0.714... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5339541 Fri, 14 Oct 2011 04:00:00 +0100 5339541 http://www.medworm.com/index.php?rid=5339540&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21999803%26dopt%3DAbstract Authors: Jalali-Heravi M, Mani-Varnosfaderani A, Jahromi PE, Mahmoodi MM, Taherinia D Abstract The main aim of the present work was to collect and categorize anti-HIV molecules in order to identify general structure-activity relationships. In this respect, a total of 5580 drugs and drug-like molecules was collected from 256 different articles published between 1992 and 2010. An algorithm called genetic algorithm-pattern search counterpropagation artificial neural networks (GPS-CPANN) was proposed for the classification of compounds. In addition, the CART (classification and regression trees) method was used for construction of decision trees and finding the best molecular descriptors. The results revealed that the developed CPANN models and decision tree can correctly classify the ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5339540 Fri, 14 Oct 2011 04:00:00 +0100 5339540 http://www.medworm.com/index.php?rid=5339539&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21999837%26dopt%3DAbstract Authors: Dimitrov S, Pavlov T, Dimitrova N, Georgieva D, Nedelcheva D, Kesova A, Vasilev R, Mekenyan O Abstract The unprecedented pollution of the environment by xenobiotic compounds has provoked the need to understand the biodegradation potential of chemicals. Mechanistic understanding of microbial degradation is a premise for adequate modelling of the environmental fate of chemicals. The aim of the present paper is to describe abiotic and biotic models implemented in CATALOGIC software. A brief overview of the specificities of abiotic and microbial degradation is provided followed by detailed descriptions of models built in our laboratory during the last decade. These are principally new models based on unique mathematical formalism already described in the first paper of this se... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5339539 Fri, 14 Oct 2011 04:00:00 +0100 5339539 http://www.medworm.com/index.php?rid=5136546&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21830879%26dopt%3DAbstract This study considered TETRATOX assay data for 85 structurally and mechanistically diverse compounds. The repeatability of replicate determinations was assessed and factors relating to repeatability are discussed. Despite the majority of compounds demonstrating excellent repeatability, it was found that the mechanism of action is likely to be a modulating factor, with compounds acting via electrophilic mechanisms being more likely to exhibit reduced repeatability than those acting via narcotic mechanisms. It is evident from this study that the TETRATOX assay is a robust and highly repeatable assay, suitable for use in toxicological modelling studies and priority setting. PMID: 21830879 [PubMed - as supplied by publisher] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5136546 Tue, 09 Aug 2011 23:00:00 +0100 5136546 http://www.medworm.com/index.php?rid=5136545&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21830880%26dopt%3DAbstract Authors: Tong J, Che T, Li Y, Wang P, Xu X, Chen Y In this work, a descriptor, SVRG (principal component scores vector of radial distribution function descriptors and geometrical descriptors), was derived from principal component analysis (PCA) of a matrix of two structural variables of coded amino acids, including radial distribution function index (RDF) and geometrical index. SVRG scales were then applied in three panels of peptide quantitative structure-activity relationships (QSARs) which were modelled by partial least squares regression (PLS). The obtained models with the correlation coefficient ([Formula: see text]), cross-validation correlation coefficient ([Formula: see text]) were 0.910 and 0.863 for 48 bitter-tasting dipeptides; 0.968 and 0.931 for 21 oxytocin analogues; and ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5136545 Tue, 09 Aug 2011 23:00:00 +0100 5136545 http://www.medworm.com/index.php?rid=5038097&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21732892%26dopt%3DAbstract Authors: Li F, Liu X, Zhang L, You L, Wu H, Li X, Zhao J, Yu J Based on the mechanism of action, a quantitative structure-activity relationship (QSAR) model for the depuration rate constants (k (d)) of 28 PAHs, 8 PBDEs and 28 PCBs in mussels (Elliptio complanata) was constructed by partial least squares (PLS) regression, following the guidelines for development and validation of QSAR models. For the training set of the QSAR model, r (2 )= 0.953, the cross-validated regression coefficient ([Formula: see text]) was 0.947. The predicted log k (d) values for the validation set were consistent with the observed values, with a standard error (SE) of 0.160 log units and a squared correlation coefficient ([Formula: see text]) of 0.892. Comparatively, the developed QSAR model had good rob... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5038097 Wed, 06 Jul 2011 23:00:00 +0100 5038097 http://www.medworm.com/index.php?rid=5038096&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21732893%26dopt%3DAbstract This study concentrates on the external validation of an existing Quantitative Structure-Activity Relationship (QSAR) model widely used for long-term aquatic toxicity to fish. In the context of the REACH legislation, QSARs are used as an alternative for experimental data to achieve a complete environmental assessment without the need for animal testing. The predictivity of the model was evaluated in order to increase the reliability of the model. We assessed whether the model met all of the OECD principles. The model was adapted to become more robust, and predictions were made with an external validation set collected from several databases. For the internal validation of the QSAR, the r (2), [Formula: see text] and [Formula: see text] were used as validation criteria, and for the external... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=5038096 Wed, 06 Jul 2011 23:00:00 +0100 5038096 http://www.medworm.com/index.php?rid=4994187&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21714732%26dopt%3DAbstract This article reports the first quantitative structure-property relationship (QSPR) for predicting the formation of TCM in chlorinated drinking water. Model compounds (n = 117) drawn from 10 literature sources were divided into training data (n = 90, analysed by five-way leave-many-out internal cross-validation) and external validation data (n = 27). QSPR internal cross-validation had Q (2 )= 0.94 and root mean square error (RMSE) of 0.09 moles TCM per mole compound, consistent with external validation Q2 of 0.94 and RMSE of 0.08 moles TCM per mole compound, and met criteria for high predictive power and robustness. In contrast, log TCM QSPR performed poorly and did not meet the criteria for predictive power. The QSPR predictions were consistent with experimental values for ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4994187 Wed, 29 Jun 2011 23:00:00 +0100 4994187 http://www.medworm.com/index.php?rid=4994186&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21714735%26dopt%3DAbstract Authors: Artemenko AG, Muratov EN, Kuz'min VE, Muratov NN, Varlamova EV, Kuz'mina AV, Gorb LG, Golius A, Hill FC, Leszczynski J, Tropsha A The Hierarchical Technology for Quantitative Structure-Activity Relationships (HiT QSAR) was applied to 95 diverse nitroaromatic compounds (including some widely known explosives) tested for their toxicity (50% inhibition growth concentration, IGC(50)) against the ciliate Tetrahymena pyriformis. The dataset was divided into subsets according to putative mechanisms of toxicity. The Classification and Regression Trees (CART) approach implemented within HiT QSAR has been used for prediction of mechanism of toxicity for new compounds. The resulting models were shown to have ∼80% accuracy for external datasets indicating that the mechanistic dataset di... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4994186 Wed, 29 Jun 2011 23:00:00 +0100 4994186 http://www.medworm.com/index.php?rid=4994185&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21714749%26dopt%3DAbstract Authors: Chen JZ, Myint KZ, Xie XQ In order to build quantitative structure-activity relationship (QSAR) models for virtual screening of novel cannabinoid CB2 ligands and hit ranking selections, a new QSAR algorithm has been developed for the cannabinoid ligands, triaryl bis-sulfones, using a combined molecular morphological and pharmacophoric search approach. Both pharmacophore features and shape complementarity were considered using a number of molecular descriptors, including Surflex-Sim similarity and Unity Query fit, in addition to other molecular properties such as molecular weight, ClogP, molecular volume, molecular area, molecular polar volume, molecular polar surface area and dipole moment. Subsequently, partial least squares regression analyses were carried out to derive QSAR... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4994185 Wed, 29 Jun 2011 23:00:00 +0100 4994185 http://www.medworm.com/index.php?rid=4631691&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21391137%26dopt%3DAbstract Authors: Sahin K, Sarıpınar E, Yanmaz E, Gecen N The electron conformational-genetic algorithm (EC-GA), a sophisticated hybrid approach combining the GA and EC methods, has been employed for a 4D-QSAR procedure to identify the pharmacophore for benzotriazines as sarcoma inhibitors and for quantitative prediction of activity. The calculated geometry and electronic structure parameters of every atom and bond of each molecule are arranged in a matrix described as the electron-conformational matrix of contiguity (ECMC). By comparing the ECMC of one of the most active compounds with other ECMCs we were able to obtain the features of the pharmacophore responsible for the activity, as submatrices of the template known as electron conformational submatrices of activity. The GA was used to se... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4631691 Wed, 09 Mar 2011 00:00:00 +0100 4631691 http://www.medworm.com/index.php?rid=4631680&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21400356%26dopt%3DAbstract Authors: Gupta AK, Bhunia SS, Balaramnavar VM, Saxena AK A pharmacophore model has been developed using diverse classes of epidermal growth factor receptor (EGFR) tyrosine kinase (TK) inhibitors useful in the treatment of human tumours. Among the top 10 generated hypotheses, the second hypothesis, with one hydrogen bond acceptor, one ring aromatic and three hydrophobic features, was found to be the best on the basis of Cat Scramble validation as well as test set prediction (r(training) = 0.89, r(test) = 0.82). The model also maps well to the external test set molecules as well as clinically active molecules and corroborates the docking studies. Finally, 10 hits were identified as potential leads after virtual screening of ZINC database for EGFR TK inhibition. The study may facilitate t... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4631680 Wed, 09 Mar 2011 00:00:00 +0100 4631680 http://www.medworm.com/index.php?rid=4631690&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21391138%26dopt%3DAbstract Authors: Natarajan R Several molecular descriptors are used in developing quantitative structure-activity relationships (QSARs). A large number of them are already in use and new descriptors are added every year. Two new topological indices with very high discriminatory power are reported in this paper. The two indices ranked all planar graphs of alkanes C(4) to C(6) uniquely and were found to have non-degenerate values for all the 7668 constitutional isomers (alkane trees) from C(4) to C(15). Low intercorrelation with several of the commonly used topological indices was studied using a diverse data set of 820 chemicals and the new indices proposed in the study were found to cluster in different nodes. This further confirmed their low intercorrelation with other molecular descriptors u... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4631690 Tue, 01 Mar 2011 00:00:00 +0100 4631690 http://www.medworm.com/index.php?rid=4631689&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21391139%26dopt%3DAbstract Authors: Jayalakshmi R, Natarajan R, Vivekanandan M Several alignment-free sequence comparison methods are available which use similarity, based on a particular numerical descriptor of biological sequences. Any loss of information incurred in the transformation of a sequence into a numerical descriptor affects the results. A pool of descriptors that use different algorithms in their computation is expected to suffer minimum loss of information and an attempt is made in this direction to study the similarity of DNA sequences. A number of descriptors based on information theory and connectivity were computed for DNA sequences. Principal component analysis (PCA) was used to extract minimum number (N) of orthogonal descriptors, principal components (PCs). Similarity/dissimilarity clusterin... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4631689 Tue, 01 Mar 2011 00:00:00 +0100 4631689 http://www.medworm.com/index.php?rid=4631688&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21391140%26dopt%3DAbstract Authors: Jensen GE, Nikolov NG, Wedebye EB, Ringsted T, Niemela JR Three modelling systems (MultiCase®, LeadScope® and MDL® QSAR) were used for construction of androgenic receptor antagonist models. There were 923-942 chemicals in the training sets. The models were cross-validated (leave-groups-out) with concordances of 77-81%, specificity of 78-91% and sensitivity of 51-76%. The specificity was highest in the MultiCase® model and the sensitivity was highest in the MDL® QSAR model. A complementary use of the models may be a valuable tool when optimizing the prediction of chemicals for androgenic receptor antagonism. When evaluating the fitness of the model for a particular application, balance of training sets, domain definition, and cut-offs for prediction interpretation should a... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4631688 Tue, 01 Mar 2011 00:00:00 +0100 4631688 http://www.medworm.com/index.php?rid=4631687&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21391141%26dopt%3DAbstract In this study, the reactivity of potential pre-electrophile polyphenolics was investigated using an in chemico assay based on glutathione (GSH) depletion; in addition, the toxicity to Tetrahymena pyriformis was determined. For pre-electrophiles, no direct relationship between toxic potency and reactivity to GSH was obtained. The structural determinants for the pre-electrophile domain were characterized qualitatively by assessing structure-activity relationships (SARs). From this analysis, structural alerts for the pre-Michael acceptor domain (i.e. non-reactive chemicals activated into Michael acceptors) were extracted from the in chemico GSH data. A series of 10 structural alerts corresponding to 1,2- and 1,4-hydroxy and amino-substituted aromatics was developed. The relevance of the alert... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4631687 Tue, 01 Mar 2011 00:00:00 +0100 4631687 http://www.medworm.com/index.php?rid=4631686&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21391142%26dopt%3DAbstract Authors: Patlewicz G, Chen MW, Bellin CA Legislation such as REACH strongly advocates the use of alternative approaches including in vitro, (Q)SARs, and chemical categories as a means to satisfy the information requirements for risk assessment. One of the most promising alternative approaches is that of chemical categories, where the underlying hypothesis is that the compounds within the category are similar and therefore should have similar biological activities. The challenge lies in characterizing the chemicals, understanding the mode/mechanism of action for the activity of interest and deriving a way of relating these together to form inferences about the likely activity outcomes. (Q)SARs are underpinned by the same hypothesis but are packaged in a more formalized manner. Since th... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4631686 Tue, 01 Mar 2011 00:00:00 +0100 4631686 http://www.medworm.com/index.php?rid=4631685&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21391143%26dopt%3DAbstract Authors: Devillers J, Mombelli E, Samsera R More than 20 years ago, Ashby and Tennant showed the interest of structural alerts for the prediction of the carcinogenicity of chemicals. These structural alerts are functional groups or structural features of various sizes that are linked to the level of carcinogenicity of chemicals. Since this pioneering work it has been possible to refine the alerts over time, as more experimental results have become available and additional mechanistic insights have been gained. To date, one of the most advanced lists of structural alerts for evaluating the carcinogenic potential of chemicals is the list proposed by Benigni and Bossa and that is implemented as a rule-based system in Toxtree and in the OECD QSAR Application Toolbox. In order to gain insig... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4631685 Tue, 01 Mar 2011 00:00:00 +0100 4631685 http://www.medworm.com/index.php?rid=4631684&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21391144%26dopt%3DAbstract The objective of this study was to predict the inhalation toxicokinetics of chemicals in mixtures using an integrated QSAR-PBPK modelling approach. The approach involved: (1) the determination of partition coefficients as well as V(max) and K(m) based solely on chemical structure for 53 volatile organic compounds, according to the group contribution approach; and (2) using the QSAR-driven coefficients as input in interaction-based PBPK models in the rat to predict the pharmacokinetics of chemicals in mixtures of up to 10 components (benzene, toluene, m-xylene, o-xylene, p-xylene, ethylbenzene, dichloromethane, trichloroethylene, tetrachloroethylene, and styrene). QSAR-estimated values of V(max) varied compared with experimental results by a factor of three for 43 out of 53 studied volatile... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4631684 Tue, 01 Mar 2011 00:00:00 +0100 4631684 http://www.medworm.com/index.php?rid=4631683&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21391145%26dopt%3DAbstract Authors: Peyret T, Krishnan K Physiologically-based pharmacokinetic (PBPK) models are increasingly finding use in risk assessment applications of data-rich compounds. However, it is a challenge to determine the chemical-specific parameters for these models, particularly in time- and resource-limiting situations. In this regard, SARs, QSARs and QPPRs are potentially useful for computing the chemical-specific input parameters of PBPK models. Based on the frequency of occurrence of molecular fragments (CH(3), CH(2), CH, C, C=C, H, benzene ring and H in benzene ring structure) and exposure conditions, the available QSAR-PBPK models facilitate the simulation of tissue and blood concentrations for some inhaled volatile organic chemicals. The application domain of existing QSARs for developin... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4631683 Tue, 01 Mar 2011 00:00:00 +0100 4631683 http://www.medworm.com/index.php?rid=4631682&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21391146%26dopt%3DAbstract Authors: Bagga V, Silakari O, Ghorela VS, Bahia MS, Rambabu G, Sarma J Interleukin-2-inducible T-cell kinase (ITK) is a key member of the Tec family of non-receptor tyrosine kinases, and has been found to be a novel target for a number of inflammatory and autoimmune diseases. A three-dimensional pharmacophore model has been generated for protein ITK from its known inhibitors. The best HypoGen model consisted of four pharmacophore features: one hydrogen bond acceptor, one hydrogen bond donor and two hydrophobic rings. This model showed a correlation coefficient of 0.947, a root mean square deviation of 0.914 and a configuration cost of 16.866. The model was validated using test set prediction and Fischer's test. A test set containing 204 compounds showed an r(2) of 0.745 between estimat... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4631682 Tue, 01 Mar 2011 00:00:00 +0100 4631682 http://www.medworm.com/index.php?rid=4631681&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21391147%26dopt%3DAbstract Authors: Rein A, Legind CN, Trapp S Models for the prediction of chemical uptake into plants are widely applied tools for human and wildlife exposure assessment, pesticide design and for environmental biotechnology such as phytoremediation. Steady-state considerations are often applied, because they are simple and have a small data need. However, often the emission pattern is non-steady. Examples are pesticide spraying, or the application of manure and sewage sludge on agricultural fields. In these scenarios, steady-state solutions are not valid, and dynamic simulation is required. We compared different approaches for dynamic modelling of plant uptake in order to identify relevant processes and timescales of processes in the soil-plant-air system. Based on the outcome, a new model conc... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4631681 Tue, 01 Mar 2011 00:00:00 +0100 4631681 http://www.medworm.com/index.php?rid=4455732&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21298820%26dopt%3DAbstract Authors: PMID: 21298820 [PubMed - indexed for MEDLINE] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4455732 Fri, 01 Oct 2010 00:00:00 +0100 4455732 http://www.medworm.com/index.php?rid=4245376&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21120750%26dopt%3DAbstract Authors: Krishnan K PMID: 21120750 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4245376 Fri, 01 Oct 2010 00:00:00 +0100 4245376 http://www.medworm.com/index.php?rid=4245375&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21120751%26dopt%3DAbstract Authors: Debia M, Krishnan K Vapour Hazard Ratio (VHR) is used in solvent substitution to select the best replacement option regarding overexposure potential of solvents. However, VHR calculations are limited by the availability of Occupational Exposure Limits (OELs). The overall objective of this study was to develop quantitative property-property relationship (QPPR) approaches for computing OELs, in view of supporting the derivation of VHRs for solvents without OELs. QPPRs were developed for estimating OELs using a database of 88 solvents which have health-based Time-Weighted Average (TWA) OELs published by the American Conference of Governmental Industrial Hygienists (ACGIH). Three surrogates of biotic lipid : air partition coefficients [n-octanol : air (K(oa)), olive oil : air (K(o... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4245375 Fri, 01 Oct 2010 00:00:00 +0100 4245375 http://www.medworm.com/index.php?rid=4245374&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21120752%26dopt%3DAbstract Authors: Ruiz P, Fowler BA, Osterloh JD, Fisher J, Mumtaz M The Agency for Toxic Substances and Disease Registry (ATSDR) is mandated by the US Congress to identify significant human exposure levels, develop methods to determine such exposures, and design strategies to mitigate them. Physiologically based pharmacokinetic (PBPK) models are increasingly being used to evaluate toxicity of environmental pollutants through multiple exposure pathways. As part of its translational research project, ATSDR is developing a human 'PBPK model tool kit' that consists of a series of published models re-coded in a common simulation language. The tool kit currently consists of models, at various stages of development, for priority environmental contaminants including solvents and persistent organic pol... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4245374 Fri, 01 Oct 2010 00:00:00 +0100 4245374 http://www.medworm.com/index.php?rid=4245373&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21120753%26dopt%3DAbstract This study has evaluated the dataset reported by Wolfreys and Basketter (Cutan. Ocul. Toxicol. 23 (2004), pp. 197-205). Upon an update of the experimental data, the original reported concordance of 68% was found to increase to 88%. There were several compounds that were 'outliers' in the two experimental evaluations which are discussed from a mechanistic basis. The discrepancies were found to be mainly associated with the differences between skin and liver metabolism. Mutagenicity information can play a significant role in evaluating sensitization potential as part of an ITS though careful attention needs to be made to ensure that any information is interpreted in the appropriate context. PMID: 21120753 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4245373 Fri, 01 Oct 2010 00:00:00 +0100 4245373 http://www.medworm.com/index.php?rid=4245372&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21120754%26dopt%3DAbstract Authors: Li J, Gramatica P Endocrine disrupting chemicals (EDCs) are suspected of posing serious threats to human and wildlife health through a variety of mechanisms, these being mainly receptor-mediated modes of action. It is reported that some EDCs exhibit dual activities as estrogen receptor (ER) and androgen receptor (AR) binders. Indeed, such compounds can affect the normal endocrine system through a dual complex mechanism, so steps should be taken not only to identify them a priori from their chemical structure, but also to prioritize them for experimental tests in order to reduce and even forbid their usage. To date, very few EDCs with dual activities have been identified. The present research uses QSARs, to investigate what, so far, is the largest and most heterogeneous ER bind... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4245372 Fri, 01 Oct 2010 00:00:00 +0100 4245372 http://www.medworm.com/index.php?rid=4245371&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21120755%26dopt%3DAbstract Authors: Dearden JC, Hewitt M Bioconcentration factor (BCF) is an important step in the uptake of environmental pollutants in the food chain. It is expensive and time-consuming to measure, so predictive methods are of value. We have used an artificial neural network QSAR approach involving descriptors for hydrophobicity, hydrogen bonding and molecular topology, obtained from commercially available software, to predict the fish BCF values of a diverse data set of 624 chemicals. The training set statistics were: r(2 )= 0.765, q(2 )= 0.763, s = 0.610, and those of the external test set were: r(2 )= 0.739, s = 0.627. The model complies with the OECD Principles for the Validation of (Q)SARs. PMID: 21120755 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4245371 Fri, 01 Oct 2010 00:00:00 +0100 4245371 http://www.medworm.com/index.php?rid=4245370&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21120756%26dopt%3DAbstract Authors: Schultz TW, Sparfkin CL, Aptula AO A diverse set of 57 heterocyclic organic chemicals, consisting of a five-membered unsaturated ring of four carbon atoms and one oxygen (furans), or sulfur (thiophenes), or nitrogen (pyrroles) were evaluated for reactivity with thiol and acute aquatic toxicity assays using glutathione (GSH) as a model nucleophile and the ciliate Tetrahymena pyriformis, respectively. Reactivity was quantified by the RC(50) value, the concentration of test compound that produced 50% reaction of the GSH thiol groups in 2 hours. Under standard conditions, RC(50) values are mathematically proportional to reciprocal rate constants. Toxicity was quantified by the IGC(50), the concentration of the test compound that produces 50% inhibition of population growth in 40 h... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4245370 Fri, 01 Oct 2010 00:00:00 +0100 4245370 http://www.medworm.com/index.php?rid=4245369&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21120757%26dopt%3DAbstract Authors: Schwobel JA, Madden JC, Cronin MT Kinetic rate constants (k(GSH)) for the reaction of compounds acting as Michael acceptors with glutathione (GSH) were modelled by quantum chemical transition-state calculations at the B3LYP/6-31G** and B3LYP/TZVP level. The data set included α, β-unsaturated aldehydes, ketones and esters, with double bonds and triple bonds, linear and cyclic systems, both with and without substituents in the α-position. Predicted values for k(GSH) were found to be in good agreement with experimental k(GSH) values. Factors affecting rate constants have been elucidated, especially solvent effects and the influence of steric hindrance. Solvent effects were examined by adding explicit solvent molecules to the system and by using a polarizable continuum solvent ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4245369 Fri, 01 Oct 2010 00:00:00 +0100 4245369 http://www.medworm.com/index.php?rid=4245368&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21120758%26dopt%3DAbstract Authors: Piir G, Sild S, Roncaglioni A, Benfenati E, Maran U The in silico modelling of bio-concentration factor (BCF) is of considerable interest in environmental sciences, because it is an accepted indicator for the accumulation potential of chemicals in organisms. Numerous QSAR models have been developed for the BCF, and the majority utilize the octanol/water partition coefficient (log P) to account for the penetration characteristics of the chemicals. The present work used descriptors from a variety of software packages for the development of a multi-linear regression model to estimate BCF. The modelled data set of 473 diverse compounds covers a wide range of log BCF values. In the proposed QSAR model, most of the variation is described by the calculated solubility in water. Other ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4245368 Fri, 01 Oct 2010 00:00:00 +0100 4245368 http://www.medworm.com/index.php?rid=4245367&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21120759%26dopt%3DAbstract Authors: Mombelli E, Devillers J The OECD (Q)SAR Application Toolbox and Toxtree are software tools used in regulatory toxicology to fill gaps in (eco)toxicity data. They include different SAR and QSAR models for estimating (eco)toxicological endpoints. Among them, the Benigni/Bossa rule-based system is proposed to characterize the carcinogenic potential of chemicals. Our study evaluates the predictive performance that can be expected from the OECD (Q)SAR Toolbox and Toxtree when analysing chemicals by means of the structural alerts coded within the Benigni/Bossa rule-based system for carcinogenicity and the associated QSAR model (QSAR8). These evaluations have been carried out thanks to a large collection of chemicals retrieved from original publications and public databases. Overall,... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4245367 Fri, 01 Oct 2010 00:00:00 +0100 4245367 http://www.medworm.com/index.php?rid=4245366&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21120760%26dopt%3DAbstract Authors: Devillers J, Mombelli E The Ames Salmonella typhimurium mutagenicity assay is a short-term bacterial reverse mutation test that was designed to detect mutagens. For several decades, it has been used in research laboratories and by regulatory agencies throughout the world for the detection and characterization of potential mutagens among natural products and man-made chemicals. Faced with the ever-growing number of chemicals available on the market, congeneric and non-congeneric (Q)SAR models have been designed from Ames test results obtained on specific S. typhimurium strains such as TA 100 or TA 98. Such models have great potential for a quick and cheap identification and classification of large numbers of potential chemical mutagens. The OECD QSAR Application Toolbox and Tox... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4245366 Fri, 01 Oct 2010 00:00:00 +0100 4245366 http://www.medworm.com/index.php?rid=4245365&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21120761%26dopt%3DAbstract Authors: Devillers J, Mombelli E The OECD QSAR Application Toolbox versions 1.1.01 and 1.1.02 and Toxtree version 1.60, which were developed for facilitating the practical use of (Q)SAR approaches by regulators, include a mechanistic SAR model for predicting the mutagenicity of α-β unsaturated aliphatic aldehydes. The aim of this study was to estimate the interest and limitations of this model. First, the model was re-computed to check its transparency and to verify its statistical validity. Then, the model implemented in the two software tools was tested on 34 chemicals not previously used for its design and for which experimental mutagenic activity data were available in the literature. A critical analysis of the results was performed and the practical interest of the model was dis... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4245365 Fri, 01 Oct 2010 00:00:00 +0100 4245365 http://www.medworm.com/index.php?rid=4245363&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21120762%26dopt%3DAbstract Authors: PMID: 21120762 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=4245363 Fri, 01 Oct 2010 00:00:00 +0100 4245363 http://www.medworm.com/index.php?rid=3948328&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20818578%26dopt%3DAbstract Authors: Qin WC, Su LM, Zhang XJ, Qin HW, Wen Y, Guo Z, Sun FT, Sheng LX, Zhao YH, Abraham MH The toxicity of organic chemicals to Vibrio fischeri, river bacteria, algae, Daphnia magna and fishes were analysed. The results showed that the toxicity of chemicals to narcotics was dependent on hydrophobicity. A single model for both polar and non-polar narcotics was developed by inclusion of a polarity descriptor as well as the hydrophobic parameter. The highly hydrophobic polar narcotics could be treated as non-polar narcotics because their polar functional group(s) make(s) a relatively small contribution to polarity as compared with their hydrophobicity. In order to investigate the toxic mechanism of action for reactive compounds, the response-surface approach was used to develop models ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3948328 Wed, 30 Jun 2010 23:00:00 +0100 3948328 http://www.medworm.com/index.php?rid=3948327&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20818579%26dopt%3DAbstract Authors: Furuhama A, Toida T, Nishikawa N, Aoki Y, Yoshioka Y, Shiraishi H The KAshinhou Tool for Ecotoxicity (KATE) system, including ecotoxicity quantitative structure-activity relationship (QSAR) models, was developed by the Japanese National Institute for Environmental Studies (NIES) using the database of aquatic toxicity results gathered by the Japanese Ministry of the Environment and the US EPA fathead minnow database. In this system chemicals can be entered according to their one-dimensional structures and classified by substructure. The QSAR equations for predicting the toxicity of a chemical compound assume a linear correlation between its log P value and its aquatic toxicity. KATE uses a structural domain called C-judgement, defined by the substructures of specified functiona... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3948327 Wed, 30 Jun 2010 23:00:00 +0100 3948327 http://www.medworm.com/index.php?rid=3948326&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20818580%26dopt%3DAbstract Authors: Boethling RS, Costanza J Knowledge of the interpolative region or applicability domain (AD) of structure-activity relationships is believed to improve predictive accuracy. The present work was undertaken to characterize the AD of EPI Suite biotransformation models and evaluate the performance of selected AD assessment methods. AD methods were applied to the training sets of four models representing different end-points, and the predictive accuracy was then evaluated using six independent validation sets. Two of the models estimated a continuous variable (log half-life) from fragment descriptors. For biotransformation in fish (BCFBAF) and hydrocarbon biodegradation (BioHCwin), the approach using ranges, with preprocessing by analysis of principal components, worked reasonably w... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3948326 Wed, 30 Jun 2010 23:00:00 +0100 3948326 http://www.medworm.com/index.php?rid=3948325&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20818581%26dopt%3DAbstract Authors: Saxena S, Chaudhaery SS, Varshney K, Saxena AK Hsp90 (Heat shock protein 90) is an important therapeutic target for the treatment of cancer. To identify important chemical features for Hsp90 inhibitory activity, a 3D-QSAR pharmacophore model was developed using a set of 61 inhibitors (a training set of 31 and a test set of 30 compounds) belonging to a series of 2-amino-6-halopurine and 7'-substituted benzothiazolothio- and pyridinothiazolothio-purines. The best HypoGen model consisted of five pharmacophoric features: one hydrogen bond acceptor (HBA), one hydrogen bond donor (HBD) and three hydrophobic (HY) groups. It showed a high correlation coefficient (r = 0.943) and low root mean square deviation (RMSD = 0.751). This model was validated against 30 known Hsp90 inhibitors, w... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3948325 Wed, 30 Jun 2010 23:00:00 +0100 3948325 http://www.medworm.com/index.php?rid=3948324&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20818582%26dopt%3DAbstract Authors: Cunningham AR, Qamar S, Carrasquer CA, Holt PA, Maguire JM, Cunningham SL, Trent JO Previously, SAR models for carcinogenesis used descriptors that are essentially chemical descriptors. Herein we report the development of models with the cat-SAR expert system using biological descriptors (i.e., ligand-receptor interactions) rat mammary carcinogens. These new descriptors are derived from the virtual screening for ligand-receptor interactions of carcinogens, non-carcinogens, and mammary carcinogens to a set of 5494 target proteins. Leave-one-out validations of the ligand mammary carcinogen-non-carcinogen model had a concordance between experimental and predicted results of 71%, and the mammary carcinogen-non-mammary carcinogen model was 72% concordant. The development of a hybri... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3948324 Wed, 30 Jun 2010 23:00:00 +0100 3948324 http://www.medworm.com/index.php?rid=3948323&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20818583%26dopt%3DAbstract Authors: Chauhan P, Shakya M Skin provides passage for the delivery of drugs. The in vitro and in vivo testing of chemicals for estimation of dermal absorption is very time consuming, costly and has many ethical difficulties related to human and animal testing. The solution to the problem is Quantitative structure-permeability relationships. This method relates dermal penetration properties of a range of chemical compounds to their physicochemical parameters. In the present study, an effort has been made to develop models for the accurate prediction of skin permeability using a large, diverse dataset through the combination of various regression methods coupled with the Genetic Algorithm (GA)/Interval Partial Least-Squares Algorithm (iPLS). The descriptors were calculated using e-DRAGO... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3948323 Wed, 30 Jun 2010 23:00:00 +0100 3948323 http://www.medworm.com/index.php?rid=3948322&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20818584%26dopt%3DAbstract Authors: Nendza M, Muller M Aquatic bioconcentration factors are critical in PBT assessment of industrial chemicals under REACH. Reliable indicators based on physico-chemical properties and molecular attributes of chemicals with low bioconcentration potential have been searched to de-prioritize non-accumulative chemicals in order to avoid unnecessary biotests that do not produce risk-relevant information. Developed to screen drug candidates, Lipinski's 'Rule of 5' identifies chemicals with poor oral absorption based on criteria in partitioning, molecular weight and hydrogen bonding. This parameter ensemble has been supplemented with molecular diameter and tested for its adequacy to filter chemicals with low bioconcentration potential. Perhaps (not) surprisingly, the application of the ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3948322 Wed, 30 Jun 2010 23:00:00 +0100 3948322 http://www.medworm.com/index.php?rid=3948321&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20818585%26dopt%3DAbstract Authors: Legind CN, Trapp S The New Model Framework (NMF) for uptake into crops is based on particle deposition and Transfer factors from soil to plant calculated from the BAse de donnees sur les teneurs en Elements Traces metalliques de Plantes Potageres (BAPPET) database. Besides NMF, approaches developed by the National Institute of Public Health and the Environment (RIVM), Hough, and the United States Environmental Protection Agency (US EPA), and the Contaminated Land Exposure Assessment (CLEA) approach were tested. Experimental data were assembled from the BAPPET database and Danish background data of As, Cd and Pb in soil, air and crops was collected. None of the models proved able to estimate the measured concentrations in plants from the BAPPET database with an absolute normali... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3948321 Wed, 30 Jun 2010 23:00:00 +0100 3948321 http://www.medworm.com/index.php?rid=3948320&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20818586%26dopt%3DAbstract Authors: Shah P, Siddiqi MI 3D-QSAR studies were carried out on a training set of 53 structurally highly diverse analogues of triclosan to investigate the correlation of the structural properties of triclosan derivatives with the inhibition of the activity of enoyl acyl carrier protein reductase in Plasmodium falciparum (PfENR) by employing Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA). The crystal structure bound conformation of triclosan, was used as a template for aligning molecules. The probable binding mode conformations of other inhibitors were explored according to molecular docking and molecular mechanics poisson-boltzmann surface area (MM/PBSA) solvation free energy estimation methods using grid based linear Poisson... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3948320 Wed, 30 Jun 2010 23:00:00 +0100 3948320 http://www.medworm.com/index.php?rid=3948319&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20818587%26dopt%3DAbstract Authors: Takahashi O, Masuda Y, Muroya A, Furuya T In general, the docking scoring tends to have a size dependence related to the ranking of compounds. In this paper, we describe a novel method of parameter optimization for docking scores which reduce the size dependence and can efficiently discriminate active compounds from chemical databases. This method is based on a simplified theoretical model of docking scores which enables us to utilize large amounts of data of known active and inactive compounds for a particular target without requiring large computational resources or a complicated procedure. This method is useful for making scoring functions for the identification of novel scaffolds using the knowledge of active compounds for a particular target or a customized scoring functi... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3948319 Wed, 30 Jun 2010 23:00:00 +0100 3948319 http://www.medworm.com/index.php?rid=3948318&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20818588%26dopt%3DAbstract In this study, we constructed a QSAR model based on a highly heterogeneous data set of 571 compounds from the US Environmental Protection Agency, for predicting acute toxicity to the fathead minnow (Pimephales promelas). An approach coupling support vector regression (SVR) with the genetic algorithm (GA) was developed to build the model. The generated QSAR model showed excellent data fitting and prediction abilities: the squared correlation coefficients (r(2)) for the training set and the test set were 0.826 and 0.802, respectively. Only eight critical descriptors, most of which are closely related to the toxicity mechanism, were chosen by GA-SVR, making the derived model readily interpretable. In summary, the successful case reported here highlights that our GA-SVR approach can be used as... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3948318 Wed, 30 Jun 2010 23:00:00 +0100 3948318 http://www.medworm.com/index.php?rid=3948317&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20818589%26dopt%3DAbstract Authors: He P Based on chaos game representation, a two-dimensional-graphical representation of protein sequences is described in which 20 amino acids are rearranged in a cyclic order using a PAM250 substitution matrix. A numerical characterisation has been developed as a descriptor to compare protein sequences. Finally, an example is given in which the dehydrogenase subunit 5 (ND5) protein sequences of nine species are compared. PMID: 20818589 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3948317 Wed, 30 Jun 2010 23:00:00 +0100 3948317 http://www.medworm.com/index.php?rid=3672465&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20544548%26dopt%3DAbstract Authors: Basak SC, Mills D Computed molecular descriptors were used to develop quantitative structure-activity relationships (QSARs) for binding affinities (K(i)) for a set of 58 cycloguanil (2,4-diamino-1,6-dihydro-1,3,5-triazine) analogues for dihydrofolate reductase (DHFR) enzyme extracted from wild and A16V+S108T mutant type (a double mutation) malaria parasite Plasmodium falciparum (Pf). High-quality models were obtained in both cases. The results of statistical analyses show that ridge regression (RR) outperformed the two other modelling methods, principal component regression (PCR) and partial least squares (PLS). For both enzymes, recognition of the inhibitors was based on four broad categories of descriptors encoding information on: (1) the electronic character of the various ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3672465 Wed, 31 Mar 2010 23:00:00 +0100 3672465 http://www.medworm.com/index.php?rid=3672464&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20544549%26dopt%3DAbstract Authors: Darnag R, Schmitzer A, Belmiloud Y, Villemin D, Jarid A, Chait A, Mazouz E, Cherqaoui D A quantitative structure-activity relationship (QSAR) study is suggested for the prediction of anti-HIV activity of tetrahydroimidazo[4,5,1-jk][1,4]benzodiazepinone (TIBO) derivatives. The model was produced by using the support vector machine (SVM) technique to develop quantitative relationships between the anti-HIV activity and ten molecular descriptors of 89 TIBO derivatives. The performance and predictive capability of the SVM method were investigated and compared with other techniques such as artificial neural networks and multiple linear regression. The results obtained indicate that the SVM model with the kernel radial basis function can be successfully used to predict the anti-HIV a... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3672464 Wed, 31 Mar 2010 23:00:00 +0100 3672464 http://www.medworm.com/index.php?rid=3672463&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20544550%26dopt%3DAbstract In this study, three marine organisms, namely Bacillus flexus (LD1), Pseudomonas fluorescens (MD3) and Vibrio natriegens (MD6), were isolated from biofilms formed on polymer and metal surfaces immersed in ocean water. Phylogenetic analysis of these three organisms indicated that they were good model systems for studying marine biofouling. The in vitro antifouling activity of 47 synthesized chalcone derivatives was investigated by estimating the minimum inhibitory concentration against these organisms using a twofold dilution technique. Compounds C-5, C-16, C-24, C-33, C-34 and C-37 were found to be the most active. In the majority of the cases it was found that these active compounds had hydroxyl substitutions. A quantitative structure-activity relationship (QSAR) was developed after divid... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3672463 Wed, 31 Mar 2010 23:00:00 +0100 3672463 http://www.medworm.com/index.php?rid=3672462&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20544551%26dopt%3DAbstract Authors: Raevsky OA, Grigor'ev VJ, Modina EA, Worth AP A modelling approach based on the structural and physicochemical similarity of chemicals to their nearest neighbours is proposed for toxicity estimation. This approach, called Arithmetic Mean Toxicity (AMT) modelling, is illustrated by means of an AMT model for predicting acute rodent toxicity. The AMT approach uses one or a few pairs of nearest structural neighbours. Each pair contains a chemical with a higher descriptor value and with a smaller descriptor value compared with the chemical of interest. Arithmetic mean toxicity values of those pairs are considered as toxicity of chemical of interest. The toxicity of the chemical of interest was not included in the development of the AMT model. The approach was applied to calculate t... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3672462 Wed, 31 Mar 2010 23:00:00 +0100 3672462 http://www.medworm.com/index.php?rid=3672461&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20544552%26dopt%3DAbstract Authors: Helguera AM, Pérez-Machado G, Cordeiro MN, Combes RD Worldwide, legislative and governmental efforts are focusing on establishing simple screening tools for identifying those chemicals most likely to cause adverse effects without experimentally testing all chemicals of regulatory concern. This is because even the most basic biological testing of compounds of concern, apart from requiring a huge number of test animals, would be neither resource nor time effective. Thus, alternative approaches such as the one proposed here, quantitative structure-activity relationship (QSAR) modelling, are increasingly being used for identifying the potential health hazards and subsequent regulation of new industrial chemicals. This paper follows up on our earlier work that demonstrated the u... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3672461 Wed, 31 Mar 2010 23:00:00 +0100 3672461 http://www.medworm.com/index.php?rid=3672460&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20544553%26dopt%3DAbstract Authors: Gunturi SB, Theerthala SS, Patel NK, Bahl J, Narayanan R Modelling of skin sensitization data of 255 diverse compounds and 450 calculated descriptors was performed to develop global predictive classification models that are applicable to whole chemical space. With this aim, we employed two automated procedures, (a) D-optimal design to select optimal members of the training and test sets and (b) k-Nearest Neighbour classification (kNN) method along with Genetic Algorithms (GA-kNN Classification) to select significant and independent descriptors in order to build the models. This methodology helped us to derive multiple models, M1-M5, that are stable and robust. The best among them, model M1 (CCR(train) = 84.3%, CCR(test) = 87.2% and CCR(ext) = 80.4%), is based on six neighbours... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3672460 Wed, 31 Mar 2010 23:00:00 +0100 3672460 http://www.medworm.com/index.php?rid=3672459&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20544554%26dopt%3DAbstract Authors: Devillers J, Devillers H, Decourtye A, Aupinel P The use of agent-based models (ABMs) is steadily increasing in all the disciplines including environmental chemistry and toxicology. This growth is mainly driven by their ability to address problems that conventional modelling techniques cannot, such as the change of scale or the emergence of unanticipated phenomena resulting from interactions between their constitutive goal-directed agents. After a brief introduction on the basic principles of agent-based modelling and the presentation of selected case studies, the main software resources available on the Internet are presented. An attempt is made to estimate the complexity of these tools versus their potentialities and flexibility. PMID: 20544554 [PubMed - in process] (Sou... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3672459 Wed, 31 Mar 2010 23:00:00 +0100 3672459 http://www.medworm.com/index.php?rid=3672458&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20544555%26dopt%3DAbstract In this study a docking study was carried out to explore the binding modes of PBDE compounds as hERalpha antagonists. It was found that some of the PBDE compounds with antiestrogenic activity extended into the channel of the estrogen receptor (ER), which is usually occupied by the alkylamine side chain of the ER antagonists raloxifene (RAL) and 4-hydroxytamoxifen (OHT), while most PBDE compounds without antiestrogenic activity adopted binding modes similar to that of ER agonist 17beta-estradiol (E2), located in the binding cavity and which did not protrude into the channel. The present study suggests that pose comparison based on docking is useful for discriminating whether or not PBDE compounds have antiestrogenic activity. Knowing the binding modes of compounds in hERalpha can help to sc... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3672458 Wed, 31 Mar 2010 23:00:00 +0100 3672458 http://www.medworm.com/index.php?rid=3672457&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20544556%26dopt%3DAbstract Authors: Sharma BK, Singh P, Sarbhai K, Prabhakar YS The serotonin 5-HT(6) binding affinity of indolyl- and piperidinyl-sulphonamide derivatives has been analysed with topological and molecular features with DRAGON software. Analysis of the structural features in conjunction with the biological endpoints in combinatorial protocol in multiple linear regression (CP-MLR) led to the identification of 25 descriptors for modelling the activity. The study clearly suggested the role of an average Randic-type eigenvector-based index from adjacency matrix, VRA2, number of secondary aliphatic amines, nNHR, the sum of the topological distance between N and O, T(N...O), ring tertiary carbon atoms, nCrHR, and CH2RX type fragment, C-006, in a molecular structure to optimize the 5-HT(6) binding affini... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3672457 Wed, 31 Mar 2010 23:00:00 +0100 3672457 http://www.medworm.com/index.php?rid=3448703&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20373211%26dopt%3DAbstract Authors: Saxena AK, Saxena S, Chaudhaery SS An adenosine tri-phosphate (ATP)-dependent molecular chaperone heat shock protein (Hsp90) is of current interest as a potential anticancer drug target. It has several oncogenic client proteins involved in signal transduction, cell cycle regulation and apoptosis. In order to identify essential chemical functional features for Hsp90 inhibition, a pharmacophore model consisting of one hydrogen bond donor, two hydrogen bond acceptor lipid and one hydrophobic feature has been developed using Hypogen (Catalyst 2.0 software) on a total set of 103 inhibitors consisting of 16 and 87 compounds in the training and the test set, respectively. The model shows good correlation for the training (r(2)= 0.887) and the test set ( [image omitted] = 0.692). In v... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3448703 Fri, 01 Jan 2010 00:00:00 +0100 3448703 http://www.medworm.com/index.php?rid=3448702&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20373212%26dopt%3DAbstract Authors: Edelstein M, Buchwald F, Richter L, Kramer S While data integration for data analysis has been investigated extensively in biological applications, it has not yet been so much the focus in computational chemistry and quantitative structure-activity relationship (QSAR) research. With the availability and growing number of chemical databases on the web, such data integration efforts become an intriguing possibility (and, in fact, a necessity). In this paper, we take a first step towards the following vision and scenario for predictive toxicology applications. Given a new structure to be predicted, the first step would be to gather (integrate) all relevant information from internet databases for the structure itself, and all structures with available information for the endpoint ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3448702 Fri, 01 Jan 2010 00:00:00 +0100 3448702 http://www.medworm.com/index.php?rid=3448701&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20373213%26dopt%3DAbstract Authors: Novoseletsky VN, Pyrkov TV, Efremov RG The adrenergic receptors mediate a wide variety of physiological responses, including vasodilatation and vasoconstriction, heart rate modulation, and others. Beta-adrenergic antagonists ('beta-blockers') thus constitute a widely used class of drugs in cardiovascular medicine as well as in management of anxiety, migraine, and glaucoma. The importance of the hydrophobic effect has been evidenced for a wide range of beta-blocker properties. To better understand the role of the hydrophobic effect in recognition of beta-blockers by their receptor, we carried out a molecular docking study combined with an original approach to estimate receptor-ligand hydrophobic interactions. The proposed method is based on automatic detection of molecular frag... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3448701 Fri, 01 Jan 2010 00:00:00 +0100 3448701 http://www.medworm.com/index.php?rid=3448700&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20373214%26dopt%3DAbstract Authors: Fjodorova N, Vracko M, Jezierska A, Novic M One of the main goals of the new chemical regulation REACH (Registration, Evaluation and Authorization of Chemicals) is to fill the gaps on the toxicological properties of chemicals that affect human health. Carcinogenicity is one of the endpoints under consideration. The information obtained from (quantitative) structure-activity relationship ((Q)SAR) models is accepted as an alternative solution to avoid expensive and time-consuming animal tests. The reported results were obtained within the framework of the European project 'Computer Assisted Evaluation of industrial chemical Substances According to Regulations (CAESAR)'. In this article, we demonstrate intermediate results for counter propagation artificial neural network (CP ANN... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3448700 Fri, 01 Jan 2010 00:00:00 +0100 3448700 http://www.medworm.com/index.php?rid=3448699&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20373215%26dopt%3DAbstract This article reviews this emerging field of studies on network dynamics in molecular biology. The basics of the CA technique are discussed along with an extensive list of related software and websites. The application of CA to networks of biochemical reactions is exemplified in detail by the case studies of the mitogen-activated protein kinase (MAPK) signalling pathway, the FAS-ligand (FASL)-induced and Bcl-2-related apoptosis. The potential of the CA method to model basic pathways patterns, to identify ways to control pathway dynamics and to help in generating strategies to fight with cancer is demonstrated. The different line of CA applications presented includes the search for the best-performing network motifs, an analysis of importance for effective intracellular signalling and pathwa... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3448699 Fri, 01 Jan 2010 00:00:00 +0100 3448699 http://www.medworm.com/index.php?rid=3448698&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20373216%26dopt%3DAbstract Authors: Basak SC, Mills D, Hawkins DM, Bhattacharjee AK A wide range of mathematical descriptors that can be calculated without the use of any other experimental data except molecular structure were used to develop models to predict binary (+/-) antimalarial activity of a set of 86 4(1H)-quinolones in two strains of parasite: D6 and TM90-C2B (chloroquine and atovaquone susceptible). The quantitative structure-activity relationship for each strain was of high quality and showed good ability in predicting activity versus inactivity when applied to a data set containing well-known antimalarial drugs. PMID: 20373216 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3448698 Fri, 01 Jan 2010 00:00:00 +0100 3448698 http://www.medworm.com/index.php?rid=3448697&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20373217%26dopt%3DAbstract This study presents a new type of acute toxicity (LD(50)) prediction that enables automated assessment of the reliability of predictions (which is synonymous with the assessment of the Model Applicability Domain as defined by the Organization for Economic Cooperation and Development). Analysis involved nearly 75,000 compounds from six animal systems (acute rat toxicity after oral and intraperitoneal administration; acute mouse toxicity after oral, intraperitoneal, intravenous, and subcutaneous administration). Fragmental Partial Least Squares (PLS) with 100 bootstraps yielded baseline predictions that were automatically corrected for non-linear effects in local chemical spaces-a combination called Global, Adjusted Locally According to Similarity (GALAS) modelling methodology. Each predicti... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3448697 Fri, 01 Jan 2010 00:00:00 +0100 3448697 http://www.medworm.com/index.php?rid=3448696&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20373218%26dopt%3DAbstract Authors: Kar S, Harding AP, Roy K, Popelier PL Extensive production and utilization of aromatic aldehydes and their derivatives without proper certification is alarming with regard to environmental safety. This concern motivated our construction of predictive quantitative structure-activity relationship (QSAR) models for the toxicity of aldehydes to the ecologically important species Tetrahymena pyriformis. Quantum topological molecular similarity (QTMS) descriptors, along with the lipid-water partition coefficient (log K(o/w)), were used as predictor variables. The QTMS descriptors were calculated at different levels of theory including AM1, HF/3-21G(d), HF/6-31G(d), B3LYP/6-31 + G(d,p), B3LYP/6-311 + G(2d,p) and MP2/6-311+G(2d,p). The data set of 77 aromatic aldehydes was divided int... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3448696 Fri, 01 Jan 2010 00:00:00 +0100 3448696 http://www.medworm.com/index.php?rid=3448695&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20373219%26dopt%3DAbstract Authors: Sharma BK, Pilania P, Singh P, Prabhakar YS The caspase-3 inhibition activity of isoquinoline-1,3,4-trione derivatives has been analysed with the topological and molecular features from Dragon software. Analysis of the structural features in conjunction with the biological endpoints in combinatorial protocol in multiple linear regression (CP-MLR) led to the identification of 45 descriptors for modelling the activity. The study clearly suggested the role of rotatable bonds, mean information on the distance degree equality, radial centricity, bond and structural information content of five-order neighbourhood symmetry, atomic van der Waals volumes and the presence or absence of certain structural fragments to optimise the caspase-3 inhibitory activity of titled compounds. The mo... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3448695 Fri, 01 Jan 2010 00:00:00 +0100 3448695 http://www.medworm.com/index.php?rid=3448694&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20373220%26dopt%3DAbstract Authors: Petkov PI, Rowlands JC, Budinsky R, Zhao B, Denison MS, Mekenyan O The aryl hydrocarbon receptor is a ligand-activated transcription factor responsive to both natural and synthetic environmental compounds, with the most potent agonist being 2,3,7,8-tetrachlotrodibenzo-p-dioxin. The aim of this work was to develop a categorical COmmon REactivity PAttern (COREPA)-based structure-activity relationship model for predicting aryl hydrocarbon receptor ligands within different binding ranges. The COREPA analysis suggested two different binding mechanisms called dioxin- and biphenyl-like, respectively. The dioxin-like model predicts a mechanism that requires a favourable interaction with a receptor nucleophilic site in the central part of the ligand and with electrophilic sites at both... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3448694 Fri, 01 Jan 2010 00:00:00 +0100 3448694 http://www.medworm.com/index.php?rid=3000331&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19916107%26dopt%3DAbstract Authors: Randic M, Vracko M, Novic M, Plavsic D We consider a spectrum-like two-dimensional graphical representation of proteins based on a reduced protein model in which 20 amino acids are grouped into five classes. This particular grouping of amino acids was suggested by Riddle and co-workers in 1997. The graphical representation is based on depicting sequentially the amino acids on five horizontal lines at equal separations. One-letter codes, B, O, U, X and Y, to which numerical values 1 to 5 have been assigned, are suggested as labels for the fictional amino acids that represent all the amino acids within each group. The approach is illustrated on ND6 proteins of eight species having from 168 to 175 amino acids. While visual inspection of the novel spectral graphical representation... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3000331 Wed, 01 Jul 2009 00:00:00 +0100 3000331 http://www.medworm.com/index.php?rid=3000330&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19916108%26dopt%3DAbstract Authors: Warne MA, Nicholson JK, Lindon JC, Guiney PD, Gartland KP A wide range of physicochemical properties based on molecular topology, size and shape, and semi-empirical molecular orbital theory were calculated for a variety of dermal and respiratory sensitizers, as well as some non-active substances. Compounds were randomly selected to belong to a training set of substances (approximately 90%) for development of quantitative structure-activity relationship (QSAR) models or to a test set (approximately 10%) for testing the models. A choice was made of those descriptors which were related to sensitization using standard statistics. Pattern recognition methods were then utilized to identify the combination of properties that provided the greatest contribution to the observed biologic... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3000330 Wed, 01 Jul 2009 00:00:00 +0100 3000330 http://www.medworm.com/index.php?rid=3000329&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19916109%26dopt%3DAbstract Authors: Fatemi MH, Abraham MH, Haghdadi M Multiple linear regression and artificial neural networks (ANNs) as feature mapping techniques were used for the prediction of the biomagnification factor (BMF) of some organochlorine pollutants. As independent variables, or compound descriptors, the Abraham descriptors often employed in linear free energy relationships were used. Much better results were obtained from the nonlinear ANN model than from multiple linear regression. The average absolute error, average relative error and root mean square error in the calculation of log (BMF) by the ANN model were 0.055, 0.051 and 0.097 for the training set and 0.11, 0.086 and 0.175 for the internal validation set, respectively. The degree of importance of each descriptor was evaluated by carrying ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3000329 Wed, 01 Jul 2009 00:00:00 +0100 3000329 http://www.medworm.com/index.php?rid=3000328&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19916110%26dopt%3DAbstract Authors: Devillers J, Devillers H With the ever-growing number of xenobiotics that can potentially contaminate the environment, the determination of their mammalian toxicity is of prime importance. In this context, LD50 tests on rats and mice have been used for a long time to express the relative hazard associated with the acute toxicity of inorganic and organic chemicals. However, these laboratory tests encounter important hurdles. They are costly, time consuming and actively opposed by animal rights activists. Moreover, new legislation policies, such as REACH (Registration, Evaluation, Authorization and Restriction of Chemicals), aim at reducing the use of toxicity tests on vertebrates. Consequently, there is a need to find alternative methods for estimating the acute mammalian toxic... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3000328 Wed, 01 Jul 2009 00:00:00 +0100 3000328 http://www.medworm.com/index.php?rid=3000327&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19916111%26dopt%3DAbstract Authors: Raevsky OA, Liplavskiy YV, Raevskaya OE, Mannhold R Stable and predictive quantitative structure-property relationship (QSPR) models of thermodynamics of chemical hydration (changes in Gibbs energy, DeltaG(air/water), enthalpy, DeltaH(air/water) and entropy DeltaS(air/water)) were obtained on the basis of physicochemical descriptors calculated by the HYBOT program. The structurally diverse training set (n = 151) and test set (n = 37) included 13 mono-functional chemical classes. The applied HYBOT descriptors comprise molecular polarizability alpha (as a volume-related term), the sum of partial negative charges on all atoms in a molecule summation operatorQ(-) (as an electrostatic term) and the sum of H-bond acceptor and donor factors summation operatorC(a) and summation operat... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3000327 Wed, 01 Jul 2009 00:00:00 +0100 3000327 http://www.medworm.com/index.php?rid=3000326&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19916112%26dopt%3DAbstract Authors: Saqib U, Siddiqi MI Three-dimensional quantitative structure-activity relationship (3D-QSAR) analyses were carried out on 45 triazolopiperazine amide derivatives as dipeptidyl peptidase IV (DPP-IV) inhibitors in order to elucidate their antidiabetic activities. The studies include Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA). Models with good predictive abilities were generated with the cross-validated r(2) ( [image omitted]) and conventional r(2) values of 0.589 and 0.868 for CoMFA and 0.586 and 0.868 for CoMSIA, respectively. Both models were validated by a test set of nine compounds and gave satisfactory predictive r(2) ( [image omitted]) values of 0.816 and 0.863, respectively. CoMFA and CoMSIA contour maps wer... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3000326 Wed, 01 Jul 2009 00:00:00 +0100 3000326 http://www.medworm.com/index.php?rid=3000325&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19916113%26dopt%3DAbstract Authors: Camargo LT, Sena MM, Camargo AJ Some indolo[2,1-b]quinalozine (tryptanthrin) analogues present cytotoxic activity against human breast cancer cells. In this work, chemometric methods were applied in the search for building discriminant models between active and inactive analogues, based on the correlations among their in vitro cytotoxic activities and their electronic and geometric molecular descriptors. From 88 descriptors calculated with density functional theory with the exchange correlation functional B3LYP and the basis set 6-31G* (Gaussian 03), 29 were pre-selected based on their Fisher weights, and finally five descriptors (partial charge on atom 15, bond orders between atoms 12-13, 17-25 and 18-26, and energy difference between frontier molecular orbitals) were selecte... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3000325 Wed, 01 Jul 2009 00:00:00 +0100 3000325 http://www.medworm.com/index.php?rid=3000324&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19916114%26dopt%3DAbstract Authors: Naik PK, Singh T, Singh H Quantitative structure-activity relationship (QSAR) analyses were performed independently on data sets belonging to two groups of insecticides, namely the organophosphates and carbamates. Several types of descriptors including topological, spatial, thermodynamic, information content, lead likeness and E-state indices were used to derive quantitative relationships between insecticide activities and structural properties of chemicals. A systematic search approach based on missing value, zero value, simple correlation and multi-collinearity tests as well as the use of a genetic algorithm allowed the optimal selection of the descriptors used to generate the models. The QSAR models developed for both organophosphate and carbamate groups revealed good predi... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3000324 Wed, 01 Jul 2009 00:00:00 +0100 3000324 http://www.medworm.com/index.php?rid=3000323&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19916115%26dopt%3DAbstract Authors: Veith GD, Petkova EP, Wallace KB This paper presents the results of an analysis of the rodent inhalation literature and the development of a quantitative structure-activity relationships (QSAR) model for 4-hour LC50 as baseline toxicity to complement the baseline toxicity model for aquatic animals. We used the same literature review criteria developed for the ECOTOX database which selects only primary references with explicit experimental methods to form a high-quality database. Our literature review focused on the primary references reporting a 4-hour exposure for a single species of rodent in which the chemical had been clearly tested as a vapour and for which the exposure concentrations were not ambiguous. An expert system was used to remove reactive chemicals, receptor-med... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3000323 Wed, 01 Jul 2009 00:00:00 +0100 3000323 http://www.medworm.com/index.php?rid=3000322&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19916116%26dopt%3DAbstract Authors: Froufe HJ, Abreu RM, Ferreira IC Wild mushrooms have been described as sources of natural antioxidants, particularly phenolic compounds. However, many other compounds present in wild mushrooms can also act as antioxidants (reducers), so whole extracts from a wide range of species need to be examined. To gain further knowledge in this area, the relationship between the antioxidant potential (scavenging effect and reducing power) and chemical composition of twenty three samples from seventeen Portuguese wild mushroom species was investigated. A wide range of analytical parameters reported by our research group (including ash, carbohydrates, proteins, fat, monounsaturated fatty acids, polyunsaturated fatty acids, saturated fatty acids, phenolics, flavonoids, ascorbic acid and bet... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3000322 Wed, 01 Jul 2009 00:00:00 +0100 3000322 http://www.medworm.com/index.php?rid=3000321&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19916117%26dopt%3DAbstract Authors: PMID: 19916117 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3000321 Wed, 01 Jul 2009 00:00:00 +0100 3000321 http://www.medworm.com/index.php?rid=3000320&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19916118%26dopt%3DAbstract Authors: PMID: 19916118 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=3000320 Wed, 01 Jul 2009 00:00:00 +0100 3000320 http://www.medworm.com/index.php?rid=2544269&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19544188%26dopt%3DAbstract Authors: Burton J, Danloy E, Vercauteren DP The evaluation of the ADME (absorption, distribution, metabolism, and excretion) properties of drug candidates is an important stage in drug discovery. To speed up the numerous tests carried out on large databases of compounds, the help of robust and accurate in silico filters is increasingly required. We propose here a method to build predictive and interpretable models for the prediction of cytochrome P450 (CYP) 1A2 and 2D6 inhibition using recursive partitioning (RP), a well-known technique for the construction of decision trees. The originality of the work is the use of several descriptions of the molecules in terms of fragments, i.e. the MACCS keys and five in-house fingerprints based on the electron density properties of fragments, empl... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2544269 Sun, 28 Jun 2009 02:07:02 +0100 2544269 http://www.medworm.com/index.php?rid=2544267&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19544189%26dopt%3DAbstract Authors: van Leeuwen K, Schultz TW, Henry T, Diderich B, Veith GD Hazard assessments of chemicals have been limited by the availability of test data and the time needed to evaluate the test data. While available data may be inadequate for the majority of industrial chemicals, the body of existing knowledge for most hazards is large enough to permit reliable estimates to be made for untested chemicals without additional animal testing. We provide a summary of the growing use by regulatory agencies of the chemical categories approach, which groups chemicals based on their similar toxicological behaviour and fills in the data gaps in animal test data such as genotoxicity and aquatic toxicity. Although the categories approach may be distinguished from the use of quantitative structure-acti... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2544267 Sun, 28 Jun 2009 02:07:02 +0100 2544267 http://www.medworm.com/index.php?rid=2544265&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19544190%26dopt%3DAbstract Authors: Haftka JJ, Parsons JR, Govers HA Strong sorption of hydrophobic organic contaminants to soot or black carbon (BC) is an important environmental process limiting the bioremediation potential of contaminated soils and sediments. Reliable methods to predict BC sorption coefficients for organic contaminants are therefore required. A computer simulation based on molecular mechanics using force field methods has been applied in this study to calculate BC sorption coefficients of polycyclic aromatic hydrocarbons (PAHs). The free energy difference between PAHs dissolved in water and in water containing a model structure of BC was calculated by thermodynamic integration of Monte Carlo simulated energies of transfer. The free energies were calculated with a hypothetical reference state ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2544265 Sun, 28 Jun 2009 02:07:02 +0100 2544265 http://www.medworm.com/index.php?rid=2544263&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19544191%26dopt%3DAbstract Authors: Dearden JC, Cronin MT, Kaiser KL Although thousands of quantitative structure-activity and structure-property relationships (QSARs/QSPRs) have been published, as well as numerous papers on the correct procedures for QSAR/QSPR analysis, many analyses are still carried out incorrectly, or in a less than satisfactory manner. We have identified 21 types of error that continue to be perpetrated in the QSAR/QSPR literature, and each of these is discussed, with examples (including some of our own). Where appropriate, we make recommendations for avoiding errors and for improving and enhancing QSAR/QSPR analyses. PMID: 19544191 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2544263 Sun, 28 Jun 2009 02:07:02 +0100 2544263 http://www.medworm.com/index.php?rid=2544261&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19544192%26dopt%3DAbstract Authors: Gharagheizi F, Sattari M A quantitative structure-property relationship (QSPR) study was performed to predict the molecular diffusivity of pure chemicals in water. A genetic-algorithm-based multivariate linear regression (GA-MLR) was applied to select the most statistically effective molecular descriptors for modelling the molecular diffusivity of pure chemicals in water. Based on the selected molecular descriptors, a three-layer feed forward neural network (FFNN) was constructed to predict the property. The obtained results showed that the FFNN was able to predict the molecular diffusivity of pure chemicals in water. PMID: 19544192 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2544261 Sun, 28 Jun 2009 02:07:02 +0100 2544261 http://www.medworm.com/index.php?rid=2544259&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19544193%26dopt%3DAbstract Authors: Gu CG, Ju XH, Jiang X, Wang F, Yang SG, Sun C With quantum chemical computation of density functional theory (DFT), the electronic properties including the polarisabilities, polarisability anisotropies and quadrupole moments of a total of 209 congeners of polybrominated diphenyl ethers (PBDEs) were evaluated. The electronic properties were shown to be highly dependent on the bromination pattern, i.e. their values changed sensitively with the number and sites of bromination. Being similar to the 2,3,7,8-, 1,4,6,9-chlorination of dioxins, respectively, 3,3',4,4'-, 2,2',5,5'-bromination of PBDEs can impose relatively greater effects on the electronic properties. Some of electronic properties were found to be potent in explaining the variance of toxicity, and the potency was verif... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2544259 Sun, 28 Jun 2009 02:07:02 +0100 2544259 http://www.medworm.com/index.php?rid=2544257&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19544194%26dopt%3DAbstract Authors: Ringsted T, Nikolov N, Jensen GE, Wedebye EB, Niemelä J Human Cytochrome P450 (CYP) is a large group of enzymes that possess an essential function in metabolising different exogenous and endogenous compounds. Humans have more than 50 different genes encoding CYP enzymes, among these a gene encoding for the CYP isoenzyme 2D6, a CYP able to metabolise drugs and other chemicals. A training set of 747 chemicals primarily based on in vivo human data for the CYP isoenzyme 2D6 was collected from the literature. QSAR models focusing on substrate/non-substrate activity were constructed by the use of MultiCASE, Leadscope and MDL quantitative structure-activity relationship (QSAR) modelling systems. They cross validated (leave-groups-out) with concordances of 71%, 81% and 82%, respe... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2544257 Sun, 28 Jun 2009 02:07:02 +0100 2544257 http://www.medworm.com/index.php?rid=2544255&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19544195%26dopt%3DAbstract Authors: Srivastava M, Singh H, Naik PK The anti-malarial activity of artemisinin-derived drugs appears to be mediated by an interaction of the drug's endoperoxide bridge with intra-parasitic haeme. The binding affinity of artemisinin analogues with haeme were computed using linear interaction energy with a surface generalised Born (LIE-SGB) continuum solvation model. Low levels of root mean square error (0.348 and 0.415 kcal/mol) as well as significant correlation coefficients (r(2) = 0.868 and 0.892) between the experimental and predicted free energy of binding (FEB) based on molecular dynamics and hybrid Monte Carlo sampling techniques establish the SGB-LIE method as an efficient tool for generating more potent inhibitors of haeme polymerisation inhibition. PMID: 19544195 [PubMe... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2544255 Sun, 28 Jun 2009 02:07:02 +0100 2544255 http://www.medworm.com/index.php?rid=2544253&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19544196%26dopt%3DAbstract Authors: Skvortsova MI, Palyulin VA, Zefirov NS A novel method is suggested for constructing topological indices (TIs) of molecular graphs which models human logic. This method is described in terms of a block scheme, consisting of the mutually connected elementary blocks. In each block the simple transformations of a molecular graph are fulfilled. A variant of the transformation is selected from the list of possible variants. Every TI is obtained as a result of the sequential execution of a number of operations, corresponding to some 'walk' on the block scheme. This walk can be selected both randomly and by the investigator. The suggested method can serve as a basis for the development of the respective computer program which may be used for the automatic construction of any number of... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2544253 Sun, 28 Jun 2009 02:07:02 +0100 2544253 http://www.medworm.com/index.php?rid=2544251&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19544197%26dopt%3DAbstract Authors: Oros G, Cserháti T The antifungal activity of 14 anthracene-based synthetic dyes and 6 reference compounds was measured on 36 fungal strains and the data matrix was evaluated separately by principal component analysis (PCA) and using a spectral mapping technique (SPM). The dimensionality of the maps of principal component loadings and variables and the selectivity maps was reduced to two by non-linear mapping. Except for two compounds, the dyes showed marked antifungal activity. Calculations proved that both the strength and selectivity of the biological effect of anthracene-based dyes were highly dependent on the chemical structure of the dye and on the type of fungi. PCA and SPM revealed different aspects of the antifungal activity, therefore, their simultaneous applica... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2544251 Sun, 28 Jun 2009 02:07:02 +0100 2544251 http://www.medworm.com/index.php?rid=2544249&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19544198%26dopt%3DAbstract Authors: Mackay D, Arnot JA, Petkova EP, Wallace KB, Call DJ, Brooke LT, Veith GD The physico-chemical properties relevant to the equilibrium partitioning (bioconcentration) of chemicals between organisms and their respired media of water and air are reviewed and illustrated for chemicals that range in hydrophobicity. Relationships are then explored between freely dissolved external concentrations such as LC50s and chemical properties for one important toxicity mechanism, namely baseline toxicity or narcosis. The 'activity hypothesis' proposed by Ferguson in 1939 provides a coherent and compelling explanation for baseline toxicity of chemicals in both water- and air-respiring organisms, as well as a reference point for identifying more specific toxicity pathways. From inhalation studie... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2544249 Sun, 28 Jun 2009 02:07:02 +0100 2544249 http://www.medworm.com/index.php?rid=2321832&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19343582%26dopt%3DAbstract Authors: Chen X, Liang YZ, Yuan DL, Xu QS To meet the requirements of providing accurate, robust, and interpretable prediction of bioactivity, a modified uncorrelated linear discriminant analysis (M-ULDA) model was developed. In addition, a feature selection method called recursive feature elimination (RFE), originally used for support vector machine (SVM), was introduced and modified to fit the scheme of ULDA. From the evaluation of six pharmaceutical datasets, the M-UDLA coupled with RFE showed better or comparable classification accuracy with respect to other well-studied methods such as SVM and decision trees. The RFE used for ULDA has the advantage of increasing the computational speed and provides useful insights into biochemical mechanisms related to pharmaceutical activity by s... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2321832 Thu, 01 Jan 2009 05:00:00 +0100 2321832 http://www.medworm.com/index.php?rid=2321828&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19343583%26dopt%3DAbstract Authors: Tan NX, Rao HB, Li ZR, Li XY In this paper we report a successful application of machine learning approaches to the prediction of chemical carcinogenicity. Two different approaches, namely a support vector machine (SVM) and artificial neural network (ANN), were evaluated for predicting chemical carcinogenicity from molecular structure descriptors. A diverse set of 844 compounds, including 600 carcinogenic (CG+) and 244 noncarcinogenic (CG-) molecules, was used to estimate the accuracies of these approaches. The database was divided into two sets: the model construction set and the independent test set. Relevant molecular descriptors were selected by a hybrid feature selection method combining Fischer's score and Monte Carlo simulated annealing from a wide set of molecular desc... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2321828 Thu, 01 Jan 2009 05:00:00 +0100 2321828 http://www.medworm.com/index.php?rid=2321824&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19343584%26dopt%3DAbstract Authors: Fatemi MH, Baher E In this work, the degradability rate constants of 98 alkenes by OH radicals were predicted from theoretically derived descriptors, which were calculated from the molecular structure alone by applying a quantitative structure-property relationship (QSPR) approach. For the selection of the most relevant descriptors, stepwise multiple linear regression (MLR) and genetic algorithms (GAs) were used. Then some linear and nonlinear techniques were used for the investigation of the relation between selected molecular descriptors and the OH radical degradability rate constant. These methods were MLR, artificial neural networks (ANNs) and support vector machines (SVMs). According to the variable selection method and feature mapping techniques, six QSPR models were con... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2321824 Thu, 01 Jan 2009 05:00:00 +0100 2321824 http://www.medworm.com/index.php?rid=2321820&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19343585%26dopt%3DAbstract Authors: Wang L, Liu XH, Wu D, Xu MZ, Sun T, Cui BS, Yang ZF Using quantum chemical descriptors and partial least squares regression, a quantitative structure-activity relationship (QSAR) model is developed for the depuration rate constants (log k(d)) of 62 polychlorinated biphenyls (PCBs) in juvenile rainbow trout (Oncorhynchus mykiss). The values of the cross-validated regression coefficient (Qcum(2)) and standard deviation (SD) are 0.655 and 0.05, respectively. The high cross-validated coefficient and low standard deviation indicate that the QSAR model is well predictive. In the QSAR model, the following six descriptors are highly significant: QH(+) (the most positive charge of a hydrogen atom), HOF (standard heat of formation), CCR (core-core repulsion), EE (electronic energy), alp... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2321820 Thu, 01 Jan 2009 05:00:00 +0100 2321820 http://www.medworm.com/index.php?rid=2321814&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19343586%26dopt%3DAbstract Authors: Kim J, Lee C, Chong Y Influenza endonucleases have appeared as an attractive target of antiviral therapy for influenza infection. With the purpose of designing a novel antiviral agent with enhanced biological activities against influenza endonuclease, a three-dimensional quantitative structure-activity relationships (3D-QSAR) model was generated based on 34 influenza endonuclease inhibitors. The comparative molecular similarity index analysis (CoMSIA) with a steric, electrostatic and hydrophobic (SEH) model showed the best correlative and predictive capability (q(2) = 0.763, r(2) = 0.969 and F = 174.785), which provided a pharmacophore composed of the electronegative moiety as well as the bulky hydrophobic group. The CoMSIA model was used as a pharmacophore query in the UNITY ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2321814 Thu, 01 Jan 2009 05:00:00 +0100 2321814 http://www.medworm.com/index.php?rid=2321809&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19343587%26dopt%3DAbstract Authors: Basak SC, Mills D In this paper a set of graph theoretic molecular descriptors was used to predict the normal vapour pressure of a collection of 121 chlorinated organic chemicals. The easily calculated topological descriptors resulted in a robust quantitative structure-property relationship (QSPR) model with q(2) of 0.988, which is comparable to a model published previously developed using the computationally expensive density functional theory (DFT) method at the B3LYP level (Becke three-parameter exchange, Lee-Yang-Parr correlation). The addition of computer-intensive quantum chemical descriptors, including polarizability, to the set of topological descriptors did not improve the predictive ability of the model. PMID: 19343587 [PubMed - in process] (Source: SAR and QSAR ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2321809 Thu, 01 Jan 2009 05:00:00 +0100 2321809 http://www.medworm.com/index.php?rid=2321803&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19343588%26dopt%3DAbstract Authors: Nikolic K, Filipic S, Agbaba D Selective imidazoline(1)-receptor (I(1)-R) ligands are used clinically to reduce blood pressure. Thus, there is significant interest in developing new imidazoline analogs with high selectivity and affinity for I(1) receptors. A quantitative structure-activity relationship (QSAR) study was carried out on 11 potent I(1)-R ligands (derivatives of imidazoline, oxazoline and pyrroline) using a multiple linear regression (MLR) procedure. The selected compounds have been studied using B3LYP/3-21G(d, p) and B3LYP/6-31G(d, p) methods. Among the 42 descriptors that were considered in generating the QSAR model, three descriptors (partial atomic charges of nitrogen in the heterocyclic moiety (N-2 charge), log D and the dipole moment of the ligands) resulted ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2321803 Thu, 01 Jan 2009 05:00:00 +0100 2321803 http://www.medworm.com/index.php?rid=2321796&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19343589%26dopt%3DAbstract In this study the PBT predictions obtained from the more user-friendly PBT Profiler and the Danish(Q)SAR database for the chemicals were compared with the results taken directly from the EPI Suite software. It was found that these widely used (Q)SAR databases might have some errors and examples are provided. It was concluded that extra care must be taken when considering the use of these databases for PBT screening. In addition, to increase the likelihood of a correct prediction, data estimates from various (Q)SAR models relevant to the PBT endpoints must be compared. PMID: 19343589 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2321796 Thu, 01 Jan 2009 05:00:00 +0100 2321796 http://www.medworm.com/index.php?rid=2321791&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19343590%26dopt%3DAbstract Authors: Aladjov H, Todorov M, Schmieder P, Serafimova R, Mekenyan O, Veith G To develop quantitative structure-activity relationships (QSAR) models capable of predicting adverse effects for large chemical inventories and diverse structures, an interactive approach is presented that includes testing of strategically selected chemicals to expand the scope of a preliminary model to cover a target inventory. The goal of chemical selection in this context is to make the testing more effective in terms of adding maximal new structural information to the predictive model with minimal testing. The aim of this paper is to describe a set of algorithmic solutions and modelling techniques that can be used to efficiently select chemicals for testing to achieve a variety of goals. One purpose of ch... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=2321791 Thu, 01 Jan 2009 05:00:00 +0100 2321791 http://www.medworm.com/index.php?rid=1880056&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18853295%26dopt%3DAbstract Authors: Maunz A, Helma C We propose a new kernel, based on 2-D structural chemical similarity, that integrates activity-specific information from the training data, and a new approach to applicability domain estimation that takes feature significances and activity distributions into consideration. The new kernel provides superior results than the well-established Tanimoto kernel, and activity-sensitive feature selection enhances prediction quality. Validation of local support vector regression models based on this kernel has been preformed with three publicly available datasets from the DSSTox project. One of them (Fathead Minnow Acute Toxicity) has been already modelled by other groups, and serves as a benchmark dataset, the other two (Maximum Recommended Therapeutic Dose, IRIS Lifet... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1880056 Thu, 16 Oct 2008 12:13:12 +0100 1880056 http://www.medworm.com/index.php?rid=1880055&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18853296%26dopt%3DAbstract Authors: Spycher S, Netzeva TI, Worth AP, Escher BI A new approach for classification of uncouplers of oxidative and photophosphorylation, also suitable for screening of large chemical inventories, is introduced. Earlier fragment-based approaches for this mode of toxic action are limited to phenols but weak acids of extremely diverse chemical classes can act as uncouplers. The proposed approach overcomes the limitation to phenolic uncouplers by combining structural fragments with the global information of physico-chemical descriptors. In a top-down approach to reduce the number of candidate chemicals, firstly substructure definitions for the detection of weak acids were applied. Subsequently, conservative physico-chemical thresholds for the two most important properties for the uncoupl... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1880055 Thu, 16 Oct 2008 12:13:12 +0100 1880055 http://www.medworm.com/index.php?rid=1880054&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18853297%26dopt%3DAbstract Authors: Luan F, Si HZ, Liu HT, Wen YY, Zhang XY Quantitative structure-activity relationship models for the prediction of the mean and the maximum atmospheric degradation half-life values of persistent organic pollutants were developed based on the linear heuristic method (HM) and non-linear gene expression programming (GEP). Molecular descriptors, calculated from the structures alone, were used to represent the characteristics of the compounds. HM was used both to pre-select the whole descriptor sets and to build the linear model. GEP yielded satisfactory prediction results: the square of the correlation coefficient r(2) was 0.80 and 0.81 for the mean and maximum half-life values of the test set, and the root mean square errors were 0.448 and 0.426, respectively. The results of this ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1880054 Thu, 16 Oct 2008 12:13:12 +0100 1880054 http://www.medworm.com/index.php?rid=1880053&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18853298%26dopt%3DAbstract Authors: Kel A, Voss N, Valeev T, Stegmaier P, Kel-Margoulis O, Wingender E Different signal transduction pathways leading to the activation of transcription factors (TFs) converge at key molecules that master the regulation of many cellular processes. Such crossroads of signalling networks often appear as "Achilles Heels" causing a disease when not functioning properly. Novel computational tools are needed for analysis of the gene expression data in the context of signal transduction and gene regulatory pathways and for identification of the key nodes in the networks. An integrated computational system, ExPlain (www.biobase.de) was developed for causal interpretation of gene expression data and identification of key signalling molecules. The system utilizes data from two databases (TR... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1880053 Thu, 16 Oct 2008 12:13:12 +0100 1880053 http://www.medworm.com/index.php?rid=1880052&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18853299%26dopt%3DAbstract Authors: Patlewicz G, Jeliazkova N, Safford RJ, Worth AP, Aleksiev B Risk assessment for most human health effects is based on the threshold of a toxicological effect, usually derived from animal experiments. The Threshold of Toxicological Concern (TTC) is a concept that refers to the establishment of a level of exposure for all chemicals below which there would be no appreciable risk to human health. When carefully applied, the TTC concept can provide a means of waiving testing based on knowledge of exposure limits. Two main approaches exist; the first of these is a General Threshold of Toxicological Concern; the second approach is a TTC in relation to structural information and/or toxicological data of chemicals. The structural scheme most routinely used is that of Cramer and co-work... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1880052 Thu, 16 Oct 2008 12:13:12 +0100 1880052 http://www.medworm.com/index.php?rid=1880051&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18853300%26dopt%3DAbstract Authors: Hawkins DM, Kraker JJ, Basak SC, Mills D Traditionally, QSAR and QSPR models have been fitted by splitting the available compounds into separate learning and validation sets. The model is then fitted to the learning set and assessed using the validation set. Cross-validation (CV) uses all available compounds for both purposes, so that the full body of available information is brought to bear on both the learning and the validation portions of the study. The price paid for this additional information is a substantially greater computational load. A common mistake in using CV is to omit some of the repetitive computations. This mistake leads to substantial bias in the assessment. A hydroxyl radical reaction rate dataset is used to illustrate the superiority of CV and the pitfall... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1880051 Thu, 16 Oct 2008 12:13:12 +0100 1880051 http://www.medworm.com/index.php?rid=1880050&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18853301%26dopt%3DAbstract Authors: Yang S, Tian F, Li Z How to extract and characterize information on molecular microstructures is deemed to be the key task to accurately simulate and predict molecular properties. In terms of atomic attributes, atoms in a molecule are divided into three levels. Based upon that, inter-atomic correlations are mapped to certain reasonable spatial coordinates in virtue of radial distribution function, generating the novel molecular graph fingerprint (MoGF), which essentially provides insight into molecular inner structures. MoGF, committing itself to transformation of molecular structures into characteristic graph curves, shows valuable advantages such as easy calculation, experimental parameters-free, rich information content, and structural significance and intuitive expressions... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1880050 Thu, 16 Oct 2008 12:13:12 +0100 1880050 http://www.medworm.com/index.php?rid=1880049&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18853302%26dopt%3DAbstract Authors: Enoch SJ, Madden JC, Cronin MT Skin sensitisation is a key endpoint under REACH as it is costly and its assessment currently has a high dependency on animal testing. In order to reduce both the cost and the numbers of animals tested, it is likely that (quantitative) structure-activity relationships ((Q)SAR) and read-across methods will be utilised as part of intelligent testing strategies. The majority of skin sensitisers elicit their effect via covalent bond formation with skin proteins. These reactions have been understood in terms of well defined nucleophilic-electrophilic reaction chemistry. Thus, a first step in (Q)SAR analysis is the assignment of a chemical's potential mechanism of action enabling it to be placed in an appropriate reactivity domain. The aim of this stud... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1880049 Thu, 16 Oct 2008 12:13:12 +0100 1880049 http://www.medworm.com/index.php?rid=1880048&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18853303%26dopt%3DAbstract This article summarizes the workshop report by highlighting the importance of continued QSAR research, the current state of VFAR science, and the guidance provided to the National Homeland Security Research Center and National Risk Management Research Laboratory by an expert panel for the continued use and development of computational approaches. PMID: 18853303 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1880048 Thu, 16 Oct 2008 12:13:12 +0100 1880048 http://www.medworm.com/index.php?rid=1880047&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18853304%26dopt%3DAbstract In this study, a new series of 2,5-disubstituted benzoxazoles was synthesized and their structures were elucidated by elemental analysis, MASS, (1)H-NMR, (13)C-NMR and IR spectral data. Newly and previously synthesized 2,5-disubstituted benzoxazole derivatives were evaluated for antibacterial and antifungal activity against standard strains and their drug-resistant isolates. Microbiological results showed that the compounds presented a large spectrum of activity having MIC values of 250-7.8 microg mL(-1) against the tested microorganisms. Among the newly synthesized derivatives 3-22, compound 11 was the most active against Candida krusei out of all; however, it was one dilution less potent than standard drug fluconazole. In addition, all the new and previous compounds were more active than... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1880047 Thu, 16 Oct 2008 12:13:12 +0100 1880047 http://www.medworm.com/index.php?rid=1646248&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18637284%26dopt%3DAbstract This study was undertaken to test the hypothesis that structurally similar PAHs induce similar gene expression profiles. THP-1 cells were exposed to a series of 12 selected PAHs at 50 microM for 24 hours and gene expressions profiles were analyzed using both unsupervised and supervised methods. Clustering analysis of gene expression profiles revealed that the 12 tested chemicals were grouped into five clusters. Within each cluster, the gene expression profiles are more similar to each other than to the ones outside the cluster. One-methylanthracene and 1-methylfluorene were found to have the most similar profiles; dibenzothiophene and dibenzofuran were found to share common profiles with fluorine. As expression pattern comparisons were expanded, similarity in genomic fingerprint dropped of... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1646248 Tue, 01 Apr 2008 04:00:00 +0100 1646248 http://www.medworm.com/index.php?rid=1637902&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18484496%26dopt%3DAbstract Authors: Kuz'min VE, Polischuk PG, Artemenko AG, Makan SY, Andronati SA The influence of molecular structure of 346 ligands on their affinity for 5-HT1A receptors was investigated. It was shown that the effectiveness of the proposed novel approach for interpretation of decision tree models compared favourably with the PLS method. In the context of the proposed approach, molecular fragments and their values of the relative influence on the affinity for 5-HT1A receptors were defined. PMID: 18484496 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1637902 Tue, 01 Apr 2008 04:00:00 +0100 1637902 http://www.medworm.com/index.php?rid=1454699&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18484495%26dopt%3DAbstract Authors: Huuskonen J, Livingstone DJ, Manallack DT Using a training set of 191 drug-like compounds extracted from the AQUASOL database a quantitative structure-property relationship (QSPR) study was conducted employing a set of simple structural and physicochemical properties to predict aqueous solubility. The resultant regression model comprised five parameters (ClogP, molecular weight, indicator variable for aliphatic amine groups, number of rotatable bonds and number of aromatic rings) and demonstrated acceptable statistics (r(2) = 0.87, s = 0.51, F = 243.6, n = 191). The model was applied to two test sets consisting of a drug-like set of compounds (r(2) = 0.80, s = 0.68, n = 174) and a set of agrochemicals (r(2) = 0.88, s = 0.65, n = 200). Using the established general solubility e... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1454699 Tue, 01 Apr 2008 04:00:00 +0100 1454699 http://www.medworm.com/index.php?rid=1454698&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18484496%26dopt%3DAbstract Authors: Kuz'min VE, Polischuk PG, Artemenko AG, Makan SY, Andronati SA The influence of molecular structure of 346 ligands on their affinity for 5-HT(1A) receptors was investigated. It was shown that the effectiveness of the proposed novel approach for interpretation of decision tree models compared favourably with the PLS method. In the context of the proposed approach, molecular fragments and their values of the relative influence on the affinity for 5-HT(1A) receptors were defined. PMID: 18484496 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1454698 Tue, 01 Apr 2008 04:00:00 +0100 1454698 http://www.medworm.com/index.php?rid=1454697&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18484497%26dopt%3DAbstract Authors: Rocher A, Marchand-Geneste N Five homology models for honeybee (Apis mellifera) nicotinic acetylcholine receptor (nAChR) alpha1/beta1, alpha3/beta2, alpha4/beta2, alpha6/beta2 and alpha9/alpha9 subtypes were built from the Torpedo marmorata nAChR X-ray structure. Then, imidacloprid, fipronil and their metabolites were docked into the ligand binding domain (LBD) of these receptors and the corresponding scoring functions were calculated. The binding modes of the docked compounds were carefully analysed. Finally, multivariate analyses were used for deriving structure-activity relationships based on hydrogen bond number and scoring functions between the insecticides and the nAChR models. PMID: 18484497 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1454697 Tue, 01 Apr 2008 04:00:00 +0100 1454697 http://www.medworm.com/index.php?rid=1454696&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18484498%26dopt%3DAbstract This study presents a QSAR/QSPR modelling and chemical grouping (read-across) approach to provide information on the biological properties of a group of aliphatic ethers, with accurate biological predictions restricted to those physico-chemical and (eco)toxicological properties where the performance of QSAR/QSPR has been shown to be acceptable. The mathematical methods used ranged from multivariate regression models to PLS (partial least-squares), SVM (support vector machines) and Sammon's mapping. A novel grouping approach, based on a set of key descriptors, has been proposed to give a compact picture of the structural and biological properties of the compounds, and to provide a more mechanistic basis for the interpretations of chemical groups. Besides being a straightforward case study, ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1454696 Tue, 01 Apr 2008 04:00:00 +0100 1454696 http://www.medworm.com/index.php?rid=1454695&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18484499%26dopt%3DAbstract This study reports an examination of the use of these descriptions of molecules to model a simple chemical interaction (complex formation) and a diverse set of mutagens. Both of these systems have been modelled successfully and the results are discussed. PMID: 18484499 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1454695 Tue, 01 Apr 2008 04:00:00 +0100 1454695 http://www.medworm.com/index.php?rid=1454694&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18484500%26dopt%3DAbstract Authors: Sobolev EV, Sobolev OV, Tikhonov DA An online resource has been developed for the theoretical study of hydration of biopolymers by the RISM (Reference Interaction Site Model) method, deriving from the integral equation theory of liquids. The online resource is based upon original software developed by the authors and includes all steps in studying a biopolymer with a given spatial structure and force field. It prepares the input data and carries out the RISM calculation yielding the atom-atom correlation functions of the biopolymer with water as solvent. From these functions the algorithm finds atomic partial contributions to the hydration free energy using various free energy expressions from integral equation theory. The calculated results are automatically recorded in a dat... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1454694 Tue, 01 Apr 2008 04:00:00 +0100 1454694 http://www.medworm.com/index.php?rid=1454693&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18484501%26dopt%3DAbstract Authors: Novic M, Randic M A novel representation of proteins was introduced. It is independent of arbitrary decisions with respect to the choice of labels to be assigned to the 20 natural amino acids. The approach is based on an assignment of 20 unit vectors in 20-dimensional vector space to the 20 natural amino acids. Proteins are then represented by a walk, that is, a sequence of steps in the 20-dimensional space analogous to a walk in the (x, y) plane in the case of binary strings. A straightforward numerical characterization of proteins is obtained from the distance matrix associated with the walk representing the protein in 20-dimensional space combining the information on the Euclidean distance between various amino acids in protein sequence. The Line Distance matrix offers addi... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1454693 Tue, 01 Apr 2008 04:00:00 +0100 1454693 http://www.medworm.com/index.php?rid=1454692&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18484502%26dopt%3DAbstract Authors: Randic M, Novic M, Vracko M A novel characterization of proteins is presented based on selected properties of recently introduced 20 x 20 amino acid adjacency matrix of proteins in which matrix elements count the occurrence of all 400 possible pair-wise adjacencies obtained by reading protein primary sequence from the left to the right. In particular we consider the characterization based on the sum and the difference of the rows and the corresponding columns, which characterize proteins by a pair of 20-component vectors. The approach is illustrated on a set of ND6 proteins of eight species. PMID: 18484502 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1454692 Tue, 01 Apr 2008 04:00:00 +0100 1454692 http://www.medworm.com/index.php?rid=1454691&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18484503%26dopt%3DAbstract Authors: Wang Y, Li Y, Ding J, Jiang Z, Chang Y Bioconcentration assessment is important in the scientific evaluation of risks that chemicals may pose to humans and environment and is a current focus of regulatory effort. In this work, a new QSAR model by adopting electronic topological properties and flexibility of chemicals to predict the bioconcentration factor (BCF) in fish was established based on a large number of diverse compounds. Multiple linear regression (MLR) and partial least squares (PLS) were used to build reliable QSARs, which were evaluated with internal five cross-validations [image omitted] and an external validation [image omitted]. The proposed MLR model showed reasonable predictivity of BCF (Q(cv)(2) = 0.79,Q(ex)(2) = 0.79) and included seven molecular descriptors... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1454691 Tue, 01 Apr 2008 04:00:00 +0100 1454691 http://www.medworm.com/index.php?rid=1454690&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18484504%26dopt%3DAbstract Authors: Patlewicz G, Jeliazkova N, Gallegos Saliner A, Worth AP Chemical similarity is a widely used concept in toxicology, and is based on the hypothesis that similar compounds should have similar biological activities. This forms the underlying basis for performing read-across, forming chemical groups and developing (Quantitative) Structure-Activity Relationships ((Q)SARs). Chemical similarity is often perceived as structural similarity but in fact there are a number of other approaches that can be used to assess similarity. A systematic similarity analysis usually comprises two main steps. Firstly the chemical structures to be compared need to be characterised in terms of relevant descriptors which encode their physicochemical, topological, geometrical and/or surface properties. A ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1454690 Tue, 01 Apr 2008 04:00:00 +0100 1454690 http://www.medworm.com/index.php?rid=1278193&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18311630%26dopt%3DAbstract Authors: Sitzmann M, Filippov IV, Nicklaus MC ()New data, tools and services recently made available on the web server (http://cactus.nci.nih.gov) of the Computer-Aided Drug Design (CADD) Group, NCI, NIH, developed in the context of chemoinformatics and drug development work, are presented. These tools are designed for searching for structures in very large databases of small molecules. One of them is a web service-the Chemical Structure Lookup Service (CSLS)-for very rapid structure lookup in an aggregated collection of more than 80 databases comprising more than 27 million unique structures at the time of this writing. CSLS contains pointers to the entries in toxicology-related databases, catalogues of commercially available samples, drugs, assay results data sets, and databases in s... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1278193 Tue, 01 Jan 2008 05:00:00 +0100 1278193 http://www.medworm.com/index.php?rid=1278192&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18311631%26dopt%3DAbstract Authors: Saxena AK, Alam I, Dixit A, Saxena M G-Protein coupled receptors (GPCRs), one of the most important families of drug targets, belong to the super family of integral membrane proteins characterized by seven transmembrane helices. Because they are difficult to crystallize, the three dimensional structure of these receptors have not yet been determined by X-ray crystallography, except one. In the absence of a 3-D structure, in-silico approaches for solving the structure of this class of proteins are widely used and provide valuable information for structure based drug design. There are several web servers and computer programs available that automate the modelling process of GPCRs. Some of these include Modeller, Swiss-Model server, Homer, etc. Using these tools reliable homology... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1278192 Tue, 01 Jan 2008 05:00:00 +0100 1278192 http://www.medworm.com/index.php?rid=1278191&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18311632%26dopt%3DAbstract Authors: Geronikaki A, Druzhilovsky D, Zakharov A, Poroikov V Some computational tools for medicinal chemistry freely available on the Internet were compared to examine whether the results of prediction obtained with different methods coincided or not. It was shown that the correlation coefficients varied from 0.65 to 0.90 for log P (seven methods), from 0.01 to 0.73 for aqueous solubility (four methods), and from 0.19 to 0.73 for drug-likeness (three methods). While for log P estimates, reasonable average pairwise correlation was found, for aqueous solubility and drug-likeness it was rather poor. Therefore, using computational tools freely available via the Internet, medicinal chemists should evaluate their accuracy versus experimental data for particular series of compounds. In contr... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1278191 Tue, 01 Jan 2008 05:00:00 +0100 1278191 http://www.medworm.com/index.php?rid=1278190&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18311633%26dopt%3DAbstract Authors: Kulkarni SA, Zhu J An integrated framework of data analysis has been proposed to systematically address the determination of the domain of applicability (DA) of some commercial Quantitative Structure Activity Relationship ((Q)SAR) models based on the structure of test chemicals. This framework forms one of the important steps in dealing with the growing concerns on reliability of model-based predictions on toxicity of chemicals specifically in the regulatory context. The present study uses some of the well-known mutagenicity and carcinogenicity models that are available within the Casetox (MultiCASE Inc.) and TOPKAT (Accelrys Software Inc.) programs. The approach enumerated in this paper employs chemoinformatics tools that facilitate comparisons of key structural features as w... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1278190 Tue, 01 Jan 2008 05:00:00 +0100 1278190 http://www.medworm.com/index.php?rid=1278189&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18311634%26dopt%3DAbstract Authors: Kiralj R, Ferreira MM Multidrug resistance activities pECr(50) of diverse strains of pathogenic fungus Penicillium digitatum against seven toxicants were studied by Principal Component Analysis (PCA) and Hierarchical Cluster Analysis (HCA). Fungal growth data (radii, circumferences, surface areas of fungal colonies, radius differences and ratios) in absence and presence of toxicants were used to derive eight new descriptors for 35 fungal strains. This data set was studied by PCA and HCA, and was correlated with the genome descriptor PCR for expression of gene CYP51 by Partial Least Squares (PLS) regression. Both analyses of pECr(50) data and of fungal growth data have identified baseline resistance character, origin and target fruits of the fungal strains. In addition, the ana... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1278189 Tue, 01 Jan 2008 05:00:00 +0100 1278189 http://www.medworm.com/index.php?rid=1278188&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18311635%26dopt%3DAbstract Authors: Chuman H The log P value has been the first choice for the molecular hydrophobicity descriptor in QSAR studies. However, it is still now difficult to understand the partitioning phenomenon in terms of physical chemistry. First, an attempt to understand and predict log P is addressed. We formulated a simple model that expressed by the solvent accessible surface area and the solvation energy difference between aqueous and solvent phases. Next, an application of log P in QSAR analyses of ligand-CYP (Cytochrome P450) interaction was described. Azole compounds are widely used as antifungal agents. We showed that the binding affinity of 18 azole compounds with CYP2B and CYP3A were nicely expressed by the bilinear model of log P. These results suggest that molecular hydrophobicity pl... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1278188 Tue, 01 Jan 2008 05:00:00 +0100 1278188 http://www.medworm.com/index.php?rid=1278187&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18311636%26dopt%3DAbstract Authors: Filz O, Lagunin A, Filimonov D, Poroikov V Drug-induced cardiac arrhythmia is acknowledged as a serious obstacle in successful development of new drugs. Several methods for in silico prediction of acquired long QT syndrome (LQTS) caused by the pharmacological blockade of human hERG K(+) channels are discussed in literature. We propose to use the computer program PASS, which estimates the probabilities of about 3000 biological activities, not only for prediction of hERG blockade and QT-prolongation but also for the analysis of indirect mechanisms of these actions. After addition in the PASS training set of 163 compounds with data on QT-Prolongation and re-training, it was shown that accuracy of prediction was 87.1% and 81.8% for hERG blockade and QT-prolongation, respectively. ... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1278187 Tue, 01 Jan 2008 05:00:00 +0100 1278187 http://www.medworm.com/index.php?rid=1278186&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18311637%26dopt%3DAbstract Authors: Pyrkov TV, Priestle JP, Jacoby E, Efremov RG Molecular docking is a powerful computational method that has been widely used in many biomolecular studies to predict geometry of a protein-ligand complex. However, while its conformational search algorithms are usually able to generate correct conformation of a ligand in the binding site, the scoring methods often fail to discriminate it among many false variants. We propose to treat this problem by applying more precise ligand-specific scoring filters to re-rank docking solutions. In this way specific features of interactions between protein and different types of compounds can be implicitly taken into account. New scoring functions were constructed including hydrogen bonds, hydrophobic and hydrophilic complementarity terms. Thes... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1278186 Tue, 01 Jan 2008 05:00:00 +0100 1278186 http://www.medworm.com/index.php?rid=1278185&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18311638%26dopt%3DAbstract Authors: Yildiz I, Ertan T, Bolelli K, Temiz-Arpaci O, Yalcin I, Aki E Considering the worth of developing new antibacterial agents against drug-resistant Stapylococcus aureus, the present study explores the structure-activity relationships analysis of N-(2-hydroxy-4(or 5)-nitro/aminophenyl)benzamide and phenylacetamide derivatives using classical QSAR and 3D-common-feature pharmacophore hypothese approaches. QSAR analysis revealed that the compounds possessing a methylene group between the phenyl and the carboxyamido moiety played a role for decreasing the activity. On the other side, substituent effects on position R(1) was found important for the activity and holding a substituent possessing a minimum width property on this position like as alkyl groups enhanced the activity. Moreov... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1278185 Tue, 01 Jan 2008 05:00:00 +0100 1278185 http://www.medworm.com/index.php?rid=1278184&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18311639%26dopt%3DAbstract Authors: Papa E, Pilutti P, Gramatica P Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous pollutants of high environmental concern. The experimental data of a mutagenicity test on human B-lymphoblastoid cells (alternative to the Ames bacterial test) for a set of 70 oxo-, nitro- and unsubstituted PAHs, detected in particulate matter (PM), were modelled by Quantitative Structure-Activity Relationships (QSAR) classification methods (k-NN, k-Nearest Neighbour, and CART, Classification and Regression Tree) based on different theoretical molecular descriptors selected by Genetic Algorithms. The best models were validated for predictivity both externally and internally. For external validation, Self Organizing Maps (SOM) were applied to split the original data set. The best models, devel... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1278184 Tue, 01 Jan 2008 05:00:00 +0100 1278184 http://www.medworm.com/index.php?rid=1278183&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18311640%26dopt%3DAbstract In this study, a large set of about 200 chemicals covering a broad range of structural classes was considered in order to categorize their relative binding affinity (RBA) to the androgen receptor. Classification of chemicals into four activity groups, with respect to their log RBA value, was carried out in a cascade of recursive partitioning trees, with descriptors calculated from CODESSA software and encoding topological, geometrical and quantum chemical properties. The hydrophobicity parameter (log P), Balaban index, and descriptors relying on charge distribution (maximum partial charge, nucleophilic index on oxygen atoms, charged surface area, etc.) appear to play a major role in the chemical partitioning. Separation of strongly active compounds was rather straightforward. Similarly, ab... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1278183 Tue, 01 Jan 2008 05:00:00 +0100 1278183 http://www.medworm.com/index.php?rid=1278182&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18311641%26dopt%3DAbstract Authors: Shulga DA, Oliferenko AA, Pisarev SA, Palyulin VA, Zefirov NS Two novel approaches to construct empirical schemes for partial atomic charge calculation were proposed. The charge schemes possess important benefits. First, they produce both topologically symmetrical and environment dependent charges. Second, they can be parameterised to reasonably reproduce ab initio molecular electrostatic potential (MEP), which guarantees their successful use in molecular modelling. To validate the approaches, the parameters of the proposed charge schemes were fitted to best reproduce MEP simultaneously on grids around a set of 227 diverse organic compounds. The residual errors in MEP reproduction due to calculated atomic charges were compared to those due to charges from known charge schemes.... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1278182 Tue, 01 Jan 2008 05:00:00 +0100 1278182 http://www.medworm.com/index.php?rid=1278181&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18311642%26dopt%3DAbstract Authors: Kouskoumvekaki I, Hansen NT, Björkling F, Vadlamudi SM, Jónsdóttir SO Recently we developed a model for prediction of pH-dependent aqueous solubility of drugs and drug like molecules. In the present work, the model was applied on a series of novel Histone Deacetylases (HDAC) inhibitors discovered at TopoTarget. The applicability of our model was evaluated on the series of HDAC inhibitors by use of Self-Organizing Maps (SOM) and 2D-projection of the HDAC inhibitors on the chemical space of the training data set of the artificial neural network (ANN) module. The model was refined for the particular chemical space of interest, which led to two modifications in the training data set of the ANN. The performance of the original and the two modified versions of the mod... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1278181 Tue, 01 Jan 2008 05:00:00 +0100 1278181 http://www.medworm.com/index.php?rid=1278180&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18311643%26dopt%3DAbstract Authors: Bunker A, Männistö P, St Pierre JF, Róg T, Pomorski P, Stimson L, Karttunen M Results from extensive 70 ns all-atom molecular dynamics simulations of catechol-O-methyltransferase (COMT) enzyme are reported. The simulations were performed with explicit TIP3P water and Mg(2 +) ions. Four different crystal structures of COMT, with and without different ligands, were used. These simulations are among the most extensive of their kind and as such served as a stability test for such simulations. On the methodological side we found that the initial energy minimization procedure may be a crucial step: particular hydrogen bonds may break, and this can initiate an irreversible loss of protein structure that becomes observable in longer time scales of the order of tens of n... SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1278180 Tue, 01 Jan 2008 05:00:00 +0100 1278180 http://www.medworm.com/index.php?rid=1052465&cid=s_36246_55_f&fid=36246&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18038362%26dopt%3DAbstract Comment on "Discriminating toxicant classes by mode of action: 3. Substructure indicators" (M. Nendza and M. Müller, SAR QSAR Environ. Res. 18 155 (2007)). SAR QSAR Environ Res. 2007 Dec;18(7):621-4 Authors: Von Der Ohe PC, Kühne R, Ebert RU, Schüürmann G PMID: 18038362 [PubMed - in process] (Source: SAR and QSAR in Environmental Research) SAR and QSAR in Environmental Research journals http://www.medworm.com/rss/comments.php?id=1052465 Tue, 27 Nov 2007 14:47:10 +0100 1052465