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Simultaneous attenuation and scatter corrections from the projections in small animal PET imaging
Abstract: Attenuation and scatter corrections are important in quantitative positron emission tomography (PET) imaging even in small animals such as mice and rats. In this work we describe a simple and efficient model to correct for both scatter and attenuation in a single operation. The model aims to solve the equation M=(A+F) P for the primaries P, corrected for attenuation and scatter, based on the measured coincidences M, the matrix of compensation for attenuation A and on the scatter fractions F issued from all emitting sources and contributing to M. The scatter functions are analytically calculated using Klein–Nish...
Source: Computer Methods and Programs in Biomedicine - November 8, 2012 Category: Bioinformatics Authors: Otman Sarrhini, M’hamed Bentourkia Tags: Section I: Methodology Source Type: research

A new fibre optic pulse oximeter probe for monitoring splanchnic organ arterial blood oxygen saturation
Abstract: A new, continuous method of monitoring splanchnic organ oxygen saturation (SpO2) would make the early detection of inadequate tissue oxygenation feasible, reducing the risk of hypoperfusion, severe ischaemia, and, ultimately, death. In an attempt to provide such a device, a new fibre optic based reflectance pulse oximeter probe and processing system were developed followed by an in vivo evaluation of the technology on seventeen patients undergoing elective laparotomy. Photoplethysmographic (PPG) signals of good quality and high signal-to-noise ratio were obtained from the small bowel, large bowel, liver and stoma...
Source: Computer Methods and Programs in Biomedicine - November 8, 2012 Category: Bioinformatics Authors: M. Hickey, N. Samuels, N. Randive, R. Langford, P.A. Kyriacou Tags: Section I: Methodology Source Type: research

Editorial Board
Source: Computer Methods and Programs in Biomedicine - November 8, 2012 Category: Bioinformatics Source Type: research

Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching
Conclusions: We find that regularization is not necessary to prevent overfitting and that thresholding is an effective and user-friendly way to perform feature selection. The proposed method avoids problems inherent in regularization-based approaches, comes with a set of well-interpretable parameters whose default configuration is shown to generalize well without the need for fine-tuning, and is applicable to spectra of different platforms. The R package IPPD implements the method and is available from the Bioconductor platform (http://bioconductor.fhcrc.org/help/bioc-views/devel/bioc/html/IPPD.html).
Source: BMC Bioinformatics - Latest articles - November 8, 2012 Category: Bioinformatics Authors: Martin SlawskiRene HussongAndreas TholeyThomas JakobyBarbara GregoriusAndreas HildebrandtMatthias Hein Source Type: research

Proteomics identifies differentially expressed proteins in neonatal murine thymus compared with adults
Conclusions: The demonstrated molecular changes are relevant for understanding thymus development as well as neonatal immune function, and they provide the diagnostic disease markers. Further studies will be required to describe in detail the role of the identified proteins in thymus maturation and in the specific functions of neonatal thymus.
Source: Proteome Science - November 8, 2012 Category: Bioinformatics Authors: Xinze CaiWenyue HuangYing QiaoYang ChenShuyan DuDong ChenShuang YuRuichao CheYi Jiang Source Type: research

Parameter sensitivity analysis of stochastic models: Application to catalytic reaction networks.
Abstract A general numerical methodology for parametric sensitivity analysis is proposed, which allows to determine the parameters exerting the greatest influence on the output of a stochastic computational model, especially when the knowledge about the actual value of a parameter is insufficient. An application of the procedure is performed on a model of protocell, in order to detect the kinetic rates mainly affecting the capability of a catalytic reaction network enclosed in a semi-permeable membrane to retain material from its environment and to generate a variety of molecular species within its boundaries. It i...
Source: Computational Biology and Chemistry - November 7, 2012 Category: Bioinformatics Authors: Damiani C, Filisetti A, Graudenzi A, Lecca P Tags: Comput Biol Chem Source Type: research

A comparison of E15.5 fetus and newborn rat serum proteomes
Conclusions: The serum proteomes of newborn rats and E15.5 fetuses were compared. The expression patterns of hemoglobin subunits were different at the two developmental stages, with most of the subunits having decreased expression. The majority of apolipoproteins had significantly decreased expression, while almost all identified complement proteins had increased expression. The levels of several highly abundant serum proteins also varied among littermates at these two developmental stages. This is the first study using LC-MS/MS to investigate serum proteome development.
Source: Proteome Science - November 7, 2012 Category: Bioinformatics Authors: Lilong WeiLulu JiaLisi ZhuSucan MaDan ZhangChen ShaoWei SunYouhe Gao Source Type: research

mGOASVM: Multi-label protein subcellular localization based on gene ontology and support vector machines
Conclusions: mGOASVM can efficiently predict the subcellular locations of multi-label proteins. The mGOASVM predictor is available online at http://bioinfo.eie.polyu.edu.hk/mGoaSvmServer/mGOASVM.html.
Source: BMC Bioinformatics - Latest articles - November 6, 2012 Category: Bioinformatics Authors: Shibiao WanMan-Wai MakSun-Yuan Kung Source Type: research

Smart wearable systems: Current status and future challenges
Conclusion: We conclude by identifying the future challenges facing SWS for HM.
Source: Artificial Intelligence in Medicine - November 5, 2012 Category: Bioinformatics Authors: Marie Chan, Daniel Estève, Jean-Yves Fourniols, Christophe Escriba, Eric Campo Tags: Research Articles Source Type: research

Software applications for flux balance analysis.
Abstract Flux balance analysis (FBA) is a widely used computational method for characterizing and engineering intrinsic cellular metabolism. The increasing number of its successful applications and growing popularity are possibly attributable to the availability of specific software tools for FBA. Each tool has its unique features and limitations with respect to operational environment, user-interface and supported analysis algorithms. Presented herein is an in-depth evaluation of currently available FBA applications, focusing mainly on usability, functionality, graphical representation and inter-operability. Overa...
Source: Briefings in Bioinformatics - November 5, 2012 Category: Bioinformatics Authors: Lakshmanan M, Koh G, Chung BK, Lee DY Tags: Brief Bioinform Source Type: research

MCMC-ODPR: Primer design optimization using Markov Chain Monte Carlo sampling
Conclusions: MCMC-ODPR is a useful tool for designing primers at various melting temperatures at good target coverage. By combining degeneracy with optimal primer reuse the user may increase coverage of sequences amplified by the designed primers at significantly lower costs. Our analyses showed that overall MCMC-ODPR outperformed the other primer-design programs in our study in terms of cost per covered base.
Source: BMC Bioinformatics - Latest articles - November 5, 2012 Category: Bioinformatics Authors: James KitchenJonathan MooreSarah PalmerRobin Allaby Source Type: research

PAnalyzer: A software tool for protein inference in shotgun proteomics
Conclusions: We present a software tool to deal with the ambiguities that arise in the protein inference process. Key contributions are support for MSE data analysis by ProteinLynx Global Server and technical replicates integration. PAnalyzer is an easy to use multiplatform and free software tool.
Source: BMC Bioinformatics - Latest articles - November 5, 2012 Category: Bioinformatics Authors: Gorka PrietoKerman AloriaNerea OsinaldeAsier FullaondoJesus M ArizmendiRune Matthiesen Source Type: research

Modeling and solving the dynamic patient admission scheduling problem under uncertainty
Conclusion: The metaheuristic approach proved to be a valid search method to solve dynamic problems in the healthcare domain.
Source: Artificial Intelligence in Medicine - November 2, 2012 Category: Bioinformatics Authors: Sara Ceschia, Andrea Schaerf Tags: Research Articles Source Type: research

A novel divide-and-merge classification for high dimensional datasets.
Abstract High dimensional datasets contain up to thousands of features, and can result in immense computational costs for classification tasks. Therefore, these datasets need a feature selection step before the classification process. The main idea behind feature selection is to choose a useful subset of features to significantly improve the comprehensibility of a classifier and maximize the performance of a classification algorithm. In this paper, we propose a one-per-class model for high dimensional datasets. In the proposed method, we extract different feature subsets for each class in a dataset and apply the cl...
Source: Computational Biology and Chemistry - November 1, 2012 Category: Bioinformatics Authors: Seo M, Oh S Tags: Comput Biol Chem Source Type: research

Editorial Board
Source: Artificial Intelligence in Medicine - November 1, 2012 Category: Bioinformatics Source Type: research

Identifying structural domains of proteins using clustering
Conclusions: It is encouraging that a basic method such as this performs nearly as well or better than some far more complex approaches. This suggests that protein domains are indeed for the most part simply compact regions of structure with a higher density of buried contacts within themselves than between each other. By representing the structure as a set of points or vectors in space, it allows us to break free of any artificial limitations that other approaches may depend upon.
Source: BMC Bioinformatics - Latest articles - November 1, 2012 Category: Bioinformatics Authors: Howard Feldman Source Type: research

Dynamic changes in the secondary structure of ECE-1 and XCE account for their different substrate specificities
Conclusions: Secondary structure changes of both enzymes during the simulation time revealed the importance of beta-sheet structure of R145/R723 for its binding with the terminal carboxylate group of the inhibitor. Unfolding of the alpha-helix comprising the S2' subsite residues in aECE-1 correlate well with its endopeptidase activity while their compact folding in aXCE may account for the inactivity of the enzyme towards large C-terminal containing substrates.
Source: BMC Bioinformatics - Latest articles - November 1, 2012 Category: Bioinformatics Authors: Zaheer Ul-HaqSadaf IqbalSyed Moin Source Type: research

PrePrint: Chain-RNA: A Comparative ncRNA Search Tool Based on the Two-dimensional Chain Algorithm
Noncoding RNA (ncRNA) identification is highly important to modern biology. The state-of-the-art method for ncRNA identification is based on comparative genomics, in which evolutionary conservations of sequences and secondary structures provide important evidence for ncRNA search. For ncRNAs with low sequence conservation but high structural similarity, conventional local alignment tools such as BLAST yield low sensitivity. Thus, there is a need for ncRNA search methods that can incorporate both sequence and structural similarities. We introduce chain-RNA, a pairwise structural alignment tool that can effectively locate cr...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - October 31, 2012 Category: Bioinformatics Source Type: research

PrePrint: Walks on SPR Neighborhoods
An nearest-neighbor-interchange (NNI) walk is a sequence of unrooted phylogenetic trees, T_1, T_2, ..., T_k where each consecutive pair of trees differ by a single NNI move. We give tight bounds on the length of the shortest NNI-walks that visit all trees in a subtree-prune-and-regraft (SPR) neighborhood of a given tree. For any unrooted, binary tree, $T$, on $n$ leaves, the shortest walk takes $\Theta(n^2)$ additional steps than the number of trees in the SPR neighborhood. This answers Bryant's Second Combinatorial Conjecture from the Phylogenetics Challenges List, the Isaac Newton Institute, 2011, and the Penny Ante Problem List, 2009.
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - October 31, 2012 Category: Bioinformatics Source Type: research

Denoising PCR-amplified metagenome data
Conclusions: DADA is more accurate and over an order of magnitude faster than AmpliconNoise. It eliminates the need for training data to establish error parameters, fully utilizes sequence-abundance information, and enables inclusion of context-dependent PCR error rates. It should be readily extensible to other sequencing platforms such as Illumina.
Source: BMC Bioinformatics - Latest articles - October 31, 2012 Category: Bioinformatics Authors: Michael RosenBenjamin CallahanDaniel FisherSusan Holmes Source Type: research

A novel algorithm for simultaneous SNP selection in high-dimensional genome-wide association studies
Conclusions: Simultaneous SNP selection is a challenging task. We demonstrate that our CAR score-based algorithm consistently outperforms all competing approaches, both uni- and multivariate, in terms of correctly recovered causal SNPs and SNP ranking. An R package implementing the approach as well as R code to reproduce the complete study presented here is available from http://strimmerlab.org/software/care/.
Source: BMC Bioinformatics - Latest articles - October 31, 2012 Category: Bioinformatics Authors: Verena ZuberA SilvaKorbinian Strimmer Source Type: research

Interactions of iron-sulfur clusters with small peptides: Insights into early evolution.
We present theoretical calculations exploring the sequence and conformational spaces of short peptides able to bind with high affinity the iron-sulfur cluster Fe(4)S(4). Our results indicate that it is unlikely to form stable complexes between Fe(4)S(4) and small peptides at the core of hydrothermal vents. The formation of these complexes is instead favored for peptides of at least 8 residues as they diffused together with the Fe(4)S(4) clusters toward lower temperature regions within the vent-associated temperature gradients. PMID: 23160058 [PubMed - as supplied by publisher]
Source: Computational Biology and Chemistry - October 30, 2012 Category: Bioinformatics Authors: Hong Enriquez RP, Do TN Tags: Comput Biol Chem Source Type: research

The defense response in Arabidopsis thaliana against Fusarium sporotrichioides
Conclusions: These results indicate that Arabidopsis is a host plant for F. sporotrichioides. We revealed that defense response of Arabidopsis is initiated by infection with F. sporotrichioides.
Source: Proteome Science - October 30, 2012 Category: Bioinformatics Authors: Tomoya AsanoMakoto KimuraTakumi Nishiuchi Source Type: research

Phosphoproteomic analysis reveals major default phosphorylation sites outside long intrinsically disordered regions of Arabidopsis plasma membrane proteins
Conclusions: The new phosphoproteomics data presented here, with published datasets and functional annotation, suggest a previously unexpected topology of phosphorylation in the plant plasma membrane proteins. The significance of these new insights into the so far overlooked properties of the plant plasma membrane phosphoproteome and the long disordered regions is discussed.
Source: Proteome Science - October 30, 2012 Category: Bioinformatics Authors: Claude NespoulousValérie RofidalNicolas SommererSonia HemMichel Rossignol Source Type: research

Bayesian Semiparametric Regression Models to Characterize Molecular Evolution
Conclusions: The model described here is distinguished by its ability to handle a large number of amino acid properties simultaneously, whiletaking into account that such data can be correlated. The multi-level clustering ability of the model allows for appealing interpretations of the results in terms of properties that are roughly equivalent from the standpoint of molecular evolution.
Source: BMC Bioinformatics - Latest articles - October 30, 2012 Category: Bioinformatics Authors: Saheli DattaAbel RodriguezRaquel Prado Source Type: research

ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs
Conclusions: ChopSticks can generate high-resolution deletion calls of homozygous deletions using information independent of other methods, and it is therefore useful to examine the functional impact of SVs or to infer SV generation mechanisms.
Source: BMC Bioinformatics - Latest articles - October 30, 2012 Category: Bioinformatics Authors: Tomohiro YasudaShin SuzukiMasao NagasakiSatoru Miyano Source Type: research

Multi-scale RNA comparison based on RNA triple vector curve representation
Conclusion: We provide a better visualization and analysis tool named TV-Curve of RNA, especial for long RNA, which can characterize both sequence and structure features. Additionally, based on TV-Curves representation of RNAs, a multi-scale similarity measure for RNA comparison is proposed, which can capture the local and global difference between the information of sequence and structure of RNAs. Compared with the well-known RNA comparison approaches, the proposed method is validated to be outstanding and effective in terms of non-coding RNA classification and RNA mutation. From the numerical experiments, our proposed me...
Source: BMC Bioinformatics - Latest articles - October 30, 2012 Category: Bioinformatics Authors: Ying LiMing DuanYanchun Liang Source Type: research

Efficient reconstruction of biological networks via transitive reduction on general purpose graphics processors
Conclusions: Parallel implementations of these algorithms can achieve speed-ups of two orders of magnitudecompared to their sequential counterparts. Our experiments show that: i) taking into account theedge weights improves the reconstruction quality compared to the unweighted case; ii) it isadvantageous not to distinguish between positive and negative interactions since this lowers thecomplexity of the algorithms from NP-complete to polynomial without loss of quality.
Source: BMC Bioinformatics - Latest articles - October 30, 2012 Category: Bioinformatics Authors: Dragan Bo¿na¿kiMaximilian OdenbrettAnton WijsWillem LigtenbergPeter Hilbers Source Type: research

Cascaded discrimination of normal, abnormal, and confounder classes in histopathology: Gleason grading of prostate cancer
Conclusions: Use of the CAS strategy increases the PPV for a multi-category classification system over two commonalternative strategies. In classification problems such as histopathology, where multiple class groups exist withvarying degrees of heterogeneity, the CAS system can intelligently assign class labels to objects by performingmultiple binary classifications according to domain knowledge.
Source: BMC Bioinformatics - Latest articles - October 30, 2012 Category: Bioinformatics Authors: Scott DoyleMichael FeldmanNatalie ShihJohn TomaszewskiAnant Madabhushi Source Type: research

Simple binary segmentation frameworks for identifying variation in DNA copy number
Variation in DNA copy number, due to gains and losses of chromosome segments, is common. A first step for analyzing DNA copy number data is to identify amplified or deleted regions in individuals. To locate such regions, we propose acircular binary segmentation procedure, which is based on a sequence of nested hypothesis tests, each using the Bayesian information criterion. The main advantages of our procedure are flexibility and simplicity. Our procedure is convenient for analyzing DNA copy number in two general situations.(1) When data from multiple platforms are used to studyvariation in copy number of the same individu...
Source: BMC Bioinformatics - Latest articles - October 30, 2012 Category: Bioinformatics Authors: Tae Young Yang Source Type: research

Coral: an integrated suite of visualizations for comparing clusterings
Conclusion: As a case study, we compare clusterings of a recently published protein interaction network of Arabidopsis thaliana. We use several popular algorithms to generate the network's clusterings. We find that the clusterings vary significantly and that few proteins are consistently co-clustered in all clusterings. This is evidence that several clusterings should typically be considered when evaluating clusters of genes, proteins, or sequences, and Coral can be used to perform a comprehensive analysis of these clustering ensembles.
Source: BMC Bioinformatics - Latest articles - October 29, 2012 Category: Bioinformatics Authors: Darya FilippovaAashish GadaniCarl Kingsford Source Type: research

The Shuttling Scaffold Model for Prevention of Yeast Pheromone Pathway Misactivation.
Abstract The molecular scaffold in the yeast pheromone pathway, Ste5, shuttles continuously between the nucleus and the cytoplasm. Ste5 undergoes oligomerization reaction in the nucleus. Upon pheromone stimulation, the Ste5 dimer is rapidly exported out of the nucleus and recruited to the plasma membrane for pathway activation. This clever device on part of the yeast cell is thought to prevent pathway misactivation at high enough levels of Ste5 in the absence of pheromone. We have built a spatiotemporal model of signaling in this pathway to describe its regulation. Our present work underscores the importance of spa...
Source: Bulletin of Mathematical Biology - October 27, 2012 Category: Bioinformatics Authors: Singh AP, Andries E, Edwards JS, Steinberg S Tags: Bull Math Biol Source Type: research

Combing the hairball with BioFabric: a new approach for visualization of large networks
Conclusions: BioFabric provides a novel and powerful way of looking at any size of network, including very large networks, using horizontal lines to represent nodes and vertical lines to represent edges. It is freely available as an open-source Java application.
Source: BMC Bioinformatics - Latest articles - October 27, 2012 Category: Bioinformatics Authors: William Longabaugh Source Type: research

Integrative structural modelling of the cardiac thin filament: energetics at the interface and conservation patterns reveal a spotlight on period 2 of tropomyosin.
Abstract Cardiomyopathies are a major health problem, with inherited cardiomyopathies, many of which are caused by mutations in genes encoding sarcomeric proteins, constituting an ever-increasing fraction of cases. To begin to study the mechanisms by which these mutations cause disease, we have employed an integrative modelling approach to study the interactions between tropomyosin and actin. Starting from the existing blocked state model, we identified a specific zone on the actin surface which is highly favourable to support tropomyosin sliding from the blocked/closed states to the open state. We then analysed th...
Source: Bioinformatics and Biology Insights - October 26, 2012 Category: Bioinformatics Authors: Margaret Sunitha S, Mercer JA, Spudich JA, Sowdhamini R Tags: Bioinform Biol Insights Source Type: research

Isotope Coded Protein Labeling analysis of plasma specimens from acute severe dengue fever patients
Conclusion: This ICPLTM study evaluating differences between acute severe dengue plasmas and acute non-severe dengue plasmas suggests that the three proteins identified are overexpressed early in the course of the disease. Their possible use as biomarkers for the prognostic of disease severity is discussed.
Source: Proteome Science - October 26, 2012 Category: Bioinformatics Authors: Romain FragnoudJavier Yugueros-MarcosAlexandre PachotFrédéric Bedin Source Type: research

A quantitative genetic and epigenetic model of complex traits
Conclusions: It provides a new avenue for bringing chromatin inheritance into the realm of complex traits, facilitating our understanding of the means by which phenotypic variation is generated.
Source: BMC Bioinformatics - Latest articles - October 26, 2012 Category: Bioinformatics Authors: Zhong WangZuoheng WangJianxin WangYihan SuiJian ZhangDuanping LiaoRongling Wu Source Type: research

PrePrint: Improved Algorithms for Matching r-Separated Sets with Applications to Protein Structure Alignment
The Largest Common Point-set (LCP) and the Pattern Matching (PM) problems have received much attention in the fields of pattern matching, computer vision and computational biology. Perhaps the most important application of these problems is the protein structural alignment, which seeks to find a superposition of a pair of input proteins that maximizes a given protein structure similarity metric. Although it has been shown that LCP and PM are both tractable problems, the running times of existing algorithms are high-degree polynomials. Here we present novel methods for finding approximate and exact threshold-LCP and thresho...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - October 25, 2012 Category: Bioinformatics Source Type: research

Dementia and molecule of the month APP.
PMID: 23055603 [PubMed]
Source: Bioinformation - October 25, 2012 Category: Bioinformatics Authors: Shapshak P Tags: Bioinformation Source Type: research

Insilico analysis and molecular docking of resuscitation promoting factor B (RpfB) protein of Mycobacterium tuberculosis.
Abstract Invulnerability of Mycobacterium tuberculosis to various drugs and its persistency has stood as a hurdle in the race against eradication of the pathogenecity of the bacteria. Identification of novel antituberculosis compounds is highly demanding as the available drugs are resistant. The ability of the bacteria to surpass the body's defenses and adapt itself to survive for disease reactivation is contributed by secreted proteins called resuscitating promoting factors (Rpfs). These factors aid in virulence and resuscitation from dormancy of the bacteria. Sequence analysis of RpfB was performed and compounds ...
Source: Bioinformation - October 25, 2012 Category: Bioinformatics Authors: Mylliemngap BJ, Borthakur A, Velmurugan D, Bhattacharjee A Tags: Bioinformation Source Type: research

Network inference of pal-1 lineage-specific regulation in the C. elegans embryo by structural equation modeling.
Abstract The elucidation of spatial and temporal control during developmental stages is one of the central tasks for systems biology, and a variety of intracellular factors are known as regulators for specific gene expression. The activity information of those various factors is not directly reflected in their gene expression profiles. Hence, a method based on Structural Equation Modeling (SEM) is described. SEM can include the latent variables within the constructed model and infer the relationships among latent and observed variables, as a network model. An improved SEM approach for the construction of an optimal...
Source: Bioinformation - October 25, 2012 Category: Bioinformatics Authors: Aburatani S Tags: Bioinformation Source Type: research

Nilotinib based pharmacophore models for BCRABL.
Abstract Tyrosine kinase inhibitors have revolutionized the treatment of several malignancies, converting lethal diseases in a manageable aspect. Imitanib, a small molecule ABL kinase inhibitor is a highly effective therapy for early phase chronic myeloid leukemia (CML), which has constitutively active ABL kinase activity owing to the over expression of the BCR-ABL fusion protein. But some patients develop imatinib resistance, particularly in the advanced phases of CML.The discovery of resistance mechanisms of imitanib; urge forward the development of second generation drugs. Nilotinib, a second generation drug is ...
Source: Bioinformation - October 25, 2012 Category: Bioinformatics Authors: Sabitha K Tags: Bioinformation Source Type: research

Potential therapeutic drug target identification in Community Acquired-Methicillin Resistant Staphylococcus aureus (CA-MRSA) using computational analysis.
Abstract The emergence of multidrug-resistant strain of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strain has highlighted the urgent need for the alternative and effective therapeutic approach to combat the menace of this nosocomial pathogen. In the present work novel potential therapeutic drug targets have been identified through the metabolic pathways analysis. All the gene products involved in different metabolic pathways of CA-MRSA in KEGG database were searched against the proteome of Homo sapiens using the BLASTp program and the threshold of E-value was set to as 0.001. After dat...
Source: Bioinformation - October 25, 2012 Category: Bioinformatics Authors: Yadav PK, Singh G, Singh S, Gautam B, Saad EI Tags: Bioinformation Source Type: research

In-silico comparative study of inhibitory mechanism of Plant Serine Proteinase Inhibitors.
Abstract The nematodes like root-knot and cyst are plant-parasitic pest found in horticultural and agricultural crops. They do damages in the roots of plants as a result losses million tons of production. High cost of nematicides and environment safety concern has necessitated finding of some alternative methods. Under Integrated Pest Management (IPM) such problems are solving significantly by means of target gene inhibition, agrobacterium mediated transformation etc. One of this strategy use Plant Proteinase Inhibitors (PIs) gene which are used to control the proteolysis mechanism of Pest by inhibiting gut Serine ...
Source: Bioinformation - October 25, 2012 Category: Bioinformatics Authors: Siva Prasad CV, Gupta S, Gaponenko A, Dhar M Tags: Bioinformation Source Type: research

Molecular docking of (5E)-3-(2-aminoethyl)-5-(2- thienylmethylene)-1, 3-thiazolidine-2, 4-dione on HIV-1 reverse transcriptase: novel drug acting on enzyme.
Abstract The study of Human immunodeficiency virus (HIV) in humans and animal models in last 31 years suggested that it is a causative agent of AIDS. This causes serious pandemic public health concern globally. It was reported that the HIV-1 reverse transcriptase (RT) played a critical role in the life cycle of HIV. Therefore, inhibition of HIV-1RT enzyme is one of the major and potential targets in the treatment of AIDS. The enzyme (HIV-1RT) was successfully targeted by non nucleotide reverse transcriptase inhibitors (NNRTIs). But frequent application of NNRTIs led drug resistance mutation on HIV infections. There...
Source: Bioinformation - October 25, 2012 Category: Bioinformatics Authors: Seniya C, Yadav A, Uchadia K, Kumar S, Sagar N, Shrivastava P, Shrivastava S, Wadhwa G Tags: Bioinformation Source Type: research

Prediction of the three-dimensional structure of aflatoxin of Aspergillus flavus by homology modelling.
This study paves the way for generating computer molecular models for proteins whose crystal structures are not available and which would aid in detailed molecular mechanism of inhibition of aflatoxin. PMID: 23055610 [PubMed]
Source: Bioinformation - October 25, 2012 Category: Bioinformatics Authors: Kasoju A, Narasu ML, Muvva C, Subbarao BV Tags: Bioinformation Source Type: research

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.
Abstract RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific info...
Source: Bioinformation - October 25, 2012 Category: Bioinformatics Authors: Afzal M, Shahid AA, Shehzadi A, Nadeem S, Husnain T Tags: Bioinformation Source Type: research

Reliability of Quality Assessments in Research Synthesis: Securing the Highest Quality Bioinformation for HIT.
Abstract Current trends in bio-medicine include research synthesis and dissemination of bioinformation by means of health (bio) information technology (H[b] IT). Research must secure the validity and reliability of assessment tools to quantify research quality in the pursuit of the best available evidence. Our concerted work in this domain led to the revision of three instruments for that purpose, including the stringent characterization of inter-rater reliability and coefficient of agreement. It is timely and critical to advance the methodological development of the science of research synthesis by strengthening t...
Source: Bioinformation - October 25, 2012 Category: Bioinformatics Authors: Chiappelli F, Phil AB, Arora R, Phi L, Giroux A, Uyeda M, Kung J, Ramchandani M Tags: Bioinformation Source Type: research

Cloning, expression and bioinformatics analysis of ATP sulfurylase from Acidithiobacillus ferrooxidans ATCC 23270 in Escherichia coli.
Abstract Molecular studies of enzymes involved in sulfite oxidation in Acidithiobacillus ferrooxidans have not yet been developed, especially in the ATP sulfurylase (ATPS) of these acidophilus tiobacilli that have importance in biomining. This enzyme synthesizes ATP and sulfate from adenosine phosphosulfate (APS) and pyrophosphate (PPi), final stage of the sulfite oxidation by these organisms in order to obtain energy. The atpS gene (1674 bp) encoding the ATPS from Acidithiobacillus ferrooxidans ATCC 23270 was amplified using PCR, cloned in the pET101-TOPO plasmid, sequenced and expressed in Escherichia coli obtain...
Source: Bioinformation - October 25, 2012 Category: Bioinformatics Authors: Jaramillo ML, Abanto M, Quispe RL, Calderón J, Del Valle LJ, Talledo M, Ramírez P Tags: Bioinformation Source Type: research

E-Pharmacophore mapping and docking studies on Vitamin D receptor (VDR).
In this study, we engaged computer-aided methodology in combination with molecular docking and pharmacophore filtering to identify chemical compounds that can increase the synthesis of vitamin D receptor (VDR) since its lower expression leads to calcium phosphate metabolic disorders in Chronic Kidney Disease. Energy-optimized pharmacophore was mapped using available agonists for VDR. Based on the e-pharmacophore, we propose the pharmacophore features that should present in VDR agonists. The resulting pharmacophore model contains one hydrogen bond acceptor (A), one hydrogen bond donor (D) and two hydrophobic regions (H). Us...
Source: Bioinformation - October 25, 2012 Category: Bioinformatics Authors: Nagamani S, Kesavan C, Muthusamy K Tags: Bioinformation Source Type: research

Comparative analysis of Wolbachia surface protein in D. melanoagster, A. tabida and B. malayi.
Abstract Wolbachia surface protein (WSP) is an eight beta-barrel transmembrane structure which participates in host immune response, cell proliferation, pathogenicity and controlled cell death program. The protein has four extracellular loops containing hyper variable regions separated by conserved regions. The WSP structure is homologous to Neisseria surface protein (Nsp A) which has about 34% similarity including antigenic variation and hydrophilicity. Recombination has a large impact on diversity of this protein including positive selection which is major constraint on protein evolution. The molecular mechanism ...
Source: Bioinformation - October 25, 2012 Category: Bioinformatics Authors: Uday J, Puttaraju HP Tags: Bioinformation Source Type: research