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Analysis of protein chameleon sequence characteristics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Conversion of local structural state of a protein from an alpha-helix to a beta-strand is usually associated with a major change in the tertiary structure. Similar changes were observed during the self assembly of amyloidogenic proteins to form fibrils, which are implicated in severe diseases conditions, e.g., Alzheimer disease. Studies have emphasized that certain protein sequence fragments known as chameleon sequences do not have a strong preference for either helical or the extended conformations. Surprisingly, the information on the local sequence neighborhood can be used to predict their secondary at a high accura...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Ghozlane A, Joseph AP, Bornot A, de Brevern AG Tags: Bioinformation Source Type: journals

A putative nuclear growth factor-like globular nematode specific protein.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Expressed sequence tags (ESTs) are an effective approach for discovery of novel genes. In the current study, approximately 250 ESTs of the cattle parasitic nematode Setaria digitata were examined and a cDNA clone identified whose coding sequence could not be functionally annotated by searching over publicly available genome, protein, EST and STS databases. Here, we report the extensive characterization of this ORF (UP) and its homologues using a bioinformatic approach. Uncharacterized protein (SDUP) of S. digitata consists of 204 amino acids with a predicted molecular weight and isoelectric point of 22.8KDa and 9.94, r...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Dassanayake RS, Rodrigo WW, Karunanayake EH, Weerasena OV, Chandrasekharan NV Tags: Bioinformation Source Type: journals

Regulatory elements in the 5'region of 16SrRNA gene of Bacillus sp. strain SJ-101.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, computational analysis of sequence homology of 546 bp 5' region of 16SrRNA gene of Bacillus sp. strain SJ-101 resulted in identification of promoter-like sequences within the rrn gene. Using BPROM tool, the regulatory motifs like -35 and -10 boxes were mapped at 392 and 411 positions, respectively. Furthermore, the cis-acting elements as the binding sites for transcription factors (TF) cpxR and argR were identified at positions 413 and 416 at the upstream of an open reading frame (ORF). The probable functions of the putative TFs were predicted through the Uni-Prot/Swiss-Prot protein database. Search for the ...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Singh BR, Al-Khedhairy AA, Alarifi SA, Musarrat J Tags: Bioinformation Source Type: journals

Identification of Comamonas species using 16S rRNA gene sequence.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
A bacterial strain Bz02 was isolated from a water sample collected from river Gomti at the Indian city of Lucknow. We characterized the strain using 16S rRNA sequence. Phylogenetic analysis showed that the strain formed a monophyletic clade with members of the genus Comamonas. The closest phylogenetic relative was Comamonas testosteroni with 95% 16S rRNA gene sequence similarity. It is proposed that the identified strain Bz02 be assigned as the type strain of a species of the genus Comamonas (Comamonas sp Bz02) based on 16S rRNA gene sequence search in Ribosomal Database Project, small subunit rRNA and large subunit rR...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Yadav V, Prakash S, Srivastava S, Verma PC, Gupta V, Basu V, Rawat AK Tags: Bioinformation Source Type: journals

A simple approach discriminating cardio-safe drugs from toxic ones.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we have formulated few rules to assess the ability to prolong QT interval and thereby discriminate between cardiotoxic and -safe drugs. These rules have clearly determined that cardio-toxic drugs are more likely to obey Lipinski rule of 5 and Oprea lead-like rule. Moreover, the cardio-toxic drugs have been found to have in common values of -0.5 to 6.5 log P, 1-5 nitrogen atoms, up to 4 oxygen atoms, 5-27 hydrophobic atoms, and 15-53 single bonds. Matthews Correlation Coefficient with the value of 0.6 was also attained and nearly 96% of the cardio-toxic drugs were successfully covered. Thus, despite the simpl...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Falah M, Nassar T, Rayan A Tags: Bioinformation Source Type: journals

A molecular model for diacylglycerol acyltransferase from Mortierella ramanniana var. angulispora.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Acyl CoA diacylglycerol acyltransferase (DGAT, EC 2.3.120) is recognized as a key player of cellular diacylglycerol metabolism. It catalyzes the terminal, yet the committed step in triacylglycerol synthesis using diacylglycerol and fatty acyl CoA as substrates. The protein sequence of diacylglycerol acyltransferse (DGAT) Type 2B in Moretierella ramanniana var. angulispora (Protein_ID = AAK84180.1) was retrieved from GenBank. However, a structure is not yet available for this sequence. The 3D structure of DGAT Type 2B was modeled using a template structure (PDB ID: 1K30) obtained from Protein databank (PDB) identified b...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Mishra S, Dwivedi SP, Dwivedi N, Kumar A, Rawat A, Kamisaka Y Tags: Bioinformation Source Type: journals

Abyssinones and related flavonoids as potential steroidogenesis modulators.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abyssinones and related flavonoids were screened against 3 enzymes (3betaHSD, 17betaHSD and Aromatase) of steroidogenesis pathway. The virtual screening experiment shows high affinity for flavonones than their respective chalcones. A 4' -OH blocked prenylated flavonone 2b (2-(2', 2'-dimethyl chroman-6'-yl)-7-hydroxy chroman-4-one) had consistent binding affinity to all the three enzymes used in this study showing higher binding affinity to aromatase. A good correlation was observed between cytotoxic data (MCF-7, breast cancer cell line) and docking results indicating flavonone as a better steroidogenesis modulator in h...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Hatti KS, Diwakar L, Rao GV, Kush A, Reddy GC Tags: Bioinformation Source Type: journals

Prediction of MHC class I binding peptides using probability distribution functions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Binding of peptides to specific Major Histo-compatibility Complex (MHC) molecule is important for understanding immunity and has applications to vaccine discovery and design of immunotherapy. Artificial neural networks (ANN) are widely used by predictions tools to classify the peptides as binders or non-binders (BNB). However, the number of known binders to a specific MHC molecule is limited in many cases, which poses a computational challenge for prediction of BNB and hence, needs improvement in learning of ANN. Here, we describe, the application of probability distribution functions to initialize the weights and bias...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Soam SS, Khan F, Bhasker B, Mishra BN Tags: Bioinformation Source Type: journals

Role of large hydrophobic residues in proteins.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe the role of LHR in complete set of protein sequences in 15 different species. That is the distribution of LHR in different proteins of different species is reported. It is observed that the proteins prefer to have 27% of large hydrophobic residues in total and all along the sequence. It is also observed that proteins accumulate more LHR in its active sites. A window analysis on these protein sequences shows that the 27% of LHR is more frequent at window length of 45 amino acids. The influenza virus and P. falciparum show a random distribution of LHR in its proteins compared to other model organisms. PMID: 1...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Jayaraj V, Suhanya R, Vijayasarathy M, Anandagopu P, Rajasekaran E Tags: Bioinformation Source Type: journals

DECOMP: A PDB decomposition tool on the web.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The protein databank (PDB) contains high quality structural data for computational structural biology investigations. We have earlier described a fast tool (the decomp_pdb tool) for identifying and marking missing atoms and residues in PDB files. The tool also automatically decomposes PDB entries into separate files describing ligands and polypeptide chains. Here, we describe a web interface named DECOMP for the tool. Our program correctly identifies multi-monomer ligands, and the server also offers the preprocessed ligand-protein decomposition of the complete PDB for downloading (up to size: 5GB) AVAILABILITY: http://...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Ordog R, Szabadka Z, Grolmusz V Tags: Bioinformation Source Type: journals

D-MATRIX: A web tool for constructing weight matrix of conserved DNA motifs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Despite considerable efforts to date, DNA motif prediction in whole genome remains a challenge for researchers. Currently the genome wide motif prediction tools required either direct pattern sequence (for single motif) or weight matrix (for multiple motifs). Although there are known motif pattern databases and tools for genome level prediction but no tool for weight matrix construction. Considering this, we developed a D-MATRIX tool which predicts the different types of weight matrix based on user defined aligned motif sequence set and motif width. For retrieval of known motif sequences user can access the commonly us...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Sen N, Mishra M, Khan F, Meena A, Sharma A Tags: Bioinformation Source Type: journals

PINAT1.0: Protein interaction network analysis tool.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Cellular processes are regulated by interaction of various proteins i.e. multiprotein complexes and absences of these interactions are often the cause of disorder or disease. Such type of protein interactions are of great interest for drug designing. In host-parasite diseases like Tuberculosis, non-homologous proteins as drug target are first preference. Most potent drug target can be identifying among large number of non-homologous protein through protein interaction network analysis. Drug target should be those non-homologous protein which is associated with maximum number of functional proteins i.e. has highest numb...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Kushwaha SK, Shakya M Tags: Bioinformation Source Type: journals

CanGeneBase (CGB) - a database on cancer related genes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The advent of genomic and proteomic technologies in this post-genomic era has urged the researchers to develop novel research strategies against cancer by targeting the human genes that would greatly facilitate to identify more promising treatment and to develop accurate early diagnosis for cancer. To harness the power of cancer genetic information towards better treatment we have developed a cancer gene database called CanGeneBase (CGB). It is a comprehensive data collection of cancer-related genes with the intention of helping the researchers to stay on a single platform to gain exclusive information on the genes of ...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Kumar GR, Subazini TK, Subha K, Rajadurai CP, Prabakar L Tags: Bioinformation Source Type: journals

Study of codon bias perspective of fungal xylanase gene by multivariate analysis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Fungal xylanases has important applications in food, baking, pulp and paper industries in addition to various other industries. Xylanases are produced extensively by both bacterial and fungal sources and has tremendous potential of being active at extremes of temperature and pH. In the present study an effort has been made to explore the codon bias perspective of this potential enzyme using bioinformatics tools. Multivariate analysis has been used as a tool to study codon bias perspectives of xylanases. It was further observed that the codon usage of xylanases genes from different fungal sources is not similar and to r...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Shrivastava S, Poddar R, Shukla P, Mukhopadhyay K Tags: Bioinformation Source Type: journals

High temperature unfolding of Bacillus anthracis amidase-03 by molecular dynamics simulations.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The stability of amidase-03 structure (a cell wall hydrolase protein) from Bacillus anthracis was studied using classical molecular dynamics (MD) simulation. This protein (GenBank accession number: NP_844822) contains an amidase-03 domain which is known to exhibit the catalytic activity of N-acetylmuramoyl-L-alanine amidase (digesting MurNAc-Lalanine linkage of bacterial cell wall). The amidase-03 enzyme has stability at high temperature due to the core formed by the combination of several secondary structure elements made of beta-sheets. We used root-mean-square-displacement (RMSD) of the simulated structure from its ...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Sharma RD, Lynn AM, Sharma PK, Rajnee , Jawaid S Tags: Bioinformation Source Type: journals

Predicted RNA secondary structures for the conserved regions in dengue virus.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Dengue fever, dengue hemorrhagic fever and dengue shock syndrome are the prevalent mosquito borne viral infections worldwide. The dengue virus belongs to the genus flavivirus with conserved RNA domains peptidase_S7 and dexHc among its members. The secondary structures for RNA domains peptidase_S7 and DexHc are hence predicted and discussed with other known viral RNA structures to glean structural insights through comparison. PMID: 19759866 [PubMed - in process] (Source: Bioinformation)
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Somvanshi P, Seth PK Tags: Bioinformation Source Type: journals

Possible role of amyloid-beta, adenine nucleotide translocase and cyclophilin-D interaction in mitochondrial dysfunction of Alzheimer's disease.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Alzheimer's disease (AD) is a common neurodegenerative disease characterized by both extra- as well as intracellular deposition of amyloid beta peptides (Abeta). The accumulation of Abeta in mitochondria is associated with mitochondrial dysfunction and oxidative stress in AD. Recent evidences suggest the involvement of Abeta interaction with mitochondrial proteins such as cyclophilin-D (CypD) in oxidative stress, mitochondrial permeability transition (MPT) and Alzheimer's associated neurodegeneration. The present study is an effort to elucidate the molecular interaction of Abeta with other proteins involved in MPT like...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Singh P, Suman S, Chandna S, Das TK Tags: Bioinformation Source Type: journals

Comparative characterization of commercially important xylanase enzymes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, a bioinformatics and molecular modeling approach was adopted to explore properties and structure of xylanases. Physico-chemical properties were predicted and prediction of motifs, disulfide bridges and secondary structure was performed for functional characterization. Apart from these analyses, three dimensional structures were constructed and stereo-chemical quality was evaluated by different structure validation tools. Comparative catalytic site analysis and assessment was performed to extract information about the important residues. Asn72 was found to be the common residue in the active sites of the prot...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Arora N, Banerjee AK, Mutyala S, Murty US Tags: Bioinformation Source Type: journals

Prediction of nucleosome positions in the yeast genome based on matched mirror position filtering.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nucleosome positioning can affect the accessibility of the underlying DNA to the nuclear environment and as such plays an essential role in the regulation of cellular processes. Specific patterns have been found in the underlying DNA sequences of the nucleosome, and one of the most important patterns includes dinucleotides distributed every 10 to 11 base pairs. Based on this property, we propose to match each dinucleotide in the sequence against its mirror occurrences for 10 to 11 base pairs on both left-hand and right-hand sides. A large number of matches in a local region will then signify the existence of a nucleoso...
Source: Bioinformation - September 20, 2009 Category: Bioinformatics Authors: Wu Q, Wang J, Yan H Tags: Bioinformation Source Type: journals

Functional interpretation of APN receptor from M.sexta using a molecular model.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Insect pests are the major cause of damage to commercially important agricultural crops. The continuous application of synthetic pesticides resulted in severe insect resistance by plants. This causes irreversible damage to the environment. Bacillus thuringiensis (Bt) emerged as a valuable biological alternative in pest control. However, insect resistance against Bt has been reported in many cases. Insects develop resistance to insecticides through mechanisms that reduce the binding of toxins to gut receptors. Nonetheless, the molecular mechanism of insect resistance is not fully understood. Therefore, it is important t...
Source: Bioinformation - August 29, 2009 Category: Bioinformatics Authors: Singh A, Sivaprasad C Tags: Bioinformation Source Type: journals

Towards the interaction mechanism of tocopherols and tocotrienols (vitamin E) with selected metabolizing enzymes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Vitamin E is a mixture of eight compounds alpha, beta, gamma, delta- tocopherols and alpha, beta, gamma, delta- tocotrienols. Their individual role in cellular transport as antioxidants and in metabolic pathways has been highlighted in the present work. All the eight compounds have been docked with the respective metabolizing enzymes (alpha-tocopherol transfer protein (ATTP), alpha-tocopherol associated protein (TAP), P-glycoprotein (P-gly) and human serum albumin (HSA)) to understand molecular interactions for pharmacokinetics. These have been structurally aligned against the four human phospholipids in order to revea...
Source: Bioinformation - August 29, 2009 Category: Bioinformatics Authors: Upadhyay J, Misra K Tags: Bioinformation Source Type: journals

Biomarkers for early detection of high risk cancers: From gliomas to nasopharyngeal carcinoma.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Nasopharyngeal carcinoma (NpC) is a malignant disease associated with Epstein-Barr virus infection, and often diagnosed at an advanced stage. This significantly curtails patient survival. We hypothesize that a panel of biomarkers can be assembled to assess NpC incidence, early detection, and tumor progression during therapeutic intervention. Our thesis rests on a model of successfully predicting high-risk gliomas by means of a carefully crafted panel of molecular mitotic biomarkers (i.e., securin, survivin and MCM2). The strategy we propose holds strong promise for prevention and cure of NpC. The approach we propose se...
Source: Bioinformation - August 29, 2009 Category: Bioinformatics Authors: Oluwadara O, Chiappelli F Tags: Bioinformation Source Type: journals

Specific gene hypomethylation and cancer: New insights into coding region feature trends.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Giving coding region structural features a role in the hypomethylation of specific genes, the occurrence of G+C content, CpG islands, repeat and retrotransposable elements in demethylated genes related to cancer has been evaluated. A comparative analysis among different cancer types has also been performed. In this work, the inter-cancer coding region features comparative analysis carried out, show insights into what structural trends/patterns are present in the studied cancers. PMID: 19707296 [PubMed - in process] (Source: Bioinformation)
Source: Bioinformation - August 29, 2009 Category: Bioinformatics Authors: Daura-Oller E, Cabre M, Montero MA, Paternain JL, Romeu A Tags: Bioinformation Source Type: journals

A database for allergenic proteins and tools for allergenicity prediction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The AllergenPro database has developed a web-based system that will provide information about allergen in microbes, animals and plants. The database has three major parts and functions:(i) database list; (ii) allergen search; and (iii) allergenicity prediction. The database contains 2,434 allergens related information readily available in the database such as on allergens in rice microbes (712 records), animals (617 records) and plants (1,105 records). Furthermore, this database provides bioinformatics tools for allergenicity prediction. Users can search for specific allergens by various methods and can run tools for a...
Source: Bioinformation - August 29, 2009 Category: Bioinformatics Authors: Kim C, Kwon S, Lee G, Lee H, Choi J, Kim Y, Hahn J Tags: Bioinformation Source Type: journals

BatchGenAna: a batch platform for large-scale genomic analysis of mammalian small RNAs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
An increasing number of small RNAs have been discovered in mammals. However, their primary transcripts and upstream regulatory networks remain largely to be determined. Genomic analysis of small RNAs facilitates identification of their primary transcripts, and hence contributes to researches of their upstream regulatory networks. We here report a batch platform, BatchGenAna, which is specifically designed for large-scale genomic analysis of mammalian small RNAs. It can map and annotate for as many as 1000 small RNAs or 10,000 genomic loci of small RNAs at a time. It provides genomic features including RefSeq genes, mRN...
Source: Bioinformation - August 29, 2009 Category: Bioinformatics Authors: Ying X, Kim YJ, Mao Y, Liu M, Hou Y, Li H, Wang X, Zhao Y, Zhao D, Patel JM, Li W Tags: Bioinformation Source Type: journals

PBEAM: A parallel implementation of BEAM for genome-wide inference of epistatic interactions.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The software tool PBEAM provides a parallel implementation of the BEAM, which is the first algorithm for large scale epistatic interaction mapping, including genome-wide studies with hundreds of thousands of markers. BEAM describes markers and their interactions with a Bayesian partitioning model and computes the posterior probability of each marker sets via Markov Chain Monte Carlo (MCMC). PBEAM takes the advantage of simulating multiple Markov chains simultaneously. This design can efficiently reduce ~n-fold execution time in the circumstance of n CPUs. The implementation of PBEAM is based on MPI libraries. AVAILABIL...
Source: Bioinformation - August 29, 2009 Category: Bioinformatics Authors: Peng T, Du P, Li Y Tags: Bioinformation Source Type: journals

UPIC: Perl scripts to determine the number of SSR markers to run.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We introduce here the concept of Unique Pattern Informative Combinations (UPIC), a decision tool for the cost-effective design of DNA fingerprinting/genotyping experiments using simple-sequence/tandem repeat (SSR/STR) markers. After the first screening of SSR-markers tested on a subset of DNA samples, the user can apply UPIC to find marker combinations that maximize the genetic information obtained by a minimum or desirable number of markers. This allows a cost-effective planning of future experiments. We have developed Perl scripts to calculate all possible subset combinations of SSR markers, and determine based on un...
Source: Bioinformation - August 29, 2009 Category: Bioinformatics Authors: Arias RS, Ballard LL, Scheffler BE Tags: Bioinformation Source Type: journals

NASCENT: An automatic protein interaction network generation tool for non-model organisms.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Large quantity of reliable protein interaction data are available for model organisms in public depositories (e.g., MINT, DIP, HPRD, INTERACT). Most data correspond to experiments with the proteins of Saccharomyces cerevisiae, Drosophila melanogaster, Homo sapiens, Caenorhabditis elegans, Escherichia coli and Mus musculus. For other important organisms the data availability is poor or non-existent. Here we present NASCENT, a completely automatic web-based tool and also a downloadable Java program, capable of modeling and generating protein interaction networks even for non-model organisms. The tool performs protein int...
Source: Bioinformation - August 29, 2009 Category: Bioinformatics Authors: Banky D, Ordog R, Grolmusz V Tags: Bioinformation Source Type: journals

sRNATarget: a web server for prediction of bacterial sRNA targets.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In bacteria, there exist some small non-coding RNAs (sRNAs) with 40-500 nucleotides in length. Most of them function as posttranscriptional regulation of gene expression through binding to their target mRNAs, in which Hfq protein acts as RNA chaperone. With the increase of identified sRNA genes in the bacterium, prediction of sRNA targets plays a more important role in determining sRNA functions. However, there are few available computational tools for predicting sRNA targets at present. Here we introduced a web server, sRNATarget, for genome-scale prediction of bacterial sRNA targets. The server is based on a recently...
Source: Bioinformation - August 29, 2009 Category: Bioinformatics Authors: Cao Y, Zhao Y, Cha L, Ying X, Wang L, Shao N, Li W Tags: Bioinformation Source Type: journals

A comparative study on the molecular descriptors for predicting drug-likeness of small molecules.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Screening of " drug-like" molecule from the molecular database produced through high throughput techniques and their large repositories requires robust classification. In our work, a set of heuristically chosen nine molecular descriptors including four from Lipinski's rule, were used as classification parameter for screening "drug-like" molecules. The robustness of classification was compared with four fundamental descriptors of Lipinski. Back propagation neural network based classifier was applied on a database of 60000 molecules for classification of, " drug-like" and "non drug-like" molecules. Classification result ...
Source: Bioinformation - August 29, 2009 Category: Bioinformatics Authors: Mishra H, Singh N, Lahiri T, Misra K Tags: Bioinformation Source Type: journals

Finding Alu in primate genomes with AF-1.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Repetitive sequences occupy more than 40% of the human genome which is much larger compared to the 2% occupied by the coding DNA. Amongst these Alu elements are the second largest class of repeats, occupying nearly 10% of the whole genome. Alus have been implicated in many genomic processes, sometimes giving rise to aberrations while many times playing as silent player in genomic and regulatory evolution. Here we present a web server, AF1, exclusively developed for finding Alu like elements. Besides alignment based methodology, this server utilizes probabilistic scanning to find more diverged elements and employs a mor...
Source: Bioinformation - March 23, 2009 Category: Bioinformatics Authors: Shankar R, Kataria B, Mukerji M Tags: Bioinformation Source Type: journals

BrainSnail: A dynamic information display system for the Sciences.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Scientific reference management has become crucial in rapidly expanding fields of biology. Many of the reference management systems currently employed are reference centric and not object/process focused. BrainSnail is a reference management/knowledge representation application that tries to bridge disconnect between subject and reference in the fields of neuropharmacology, neuroanatomy and neurophysiology. BrainSnail has been developed with considering both individual researcher and research group efforts. PMID: 19293992 [PubMed - in process] (Source: Bioinformation)
Source: Bioinformation - March 23, 2009 Category: Bioinformatics Authors: Telefont M, Asaithambi A Tags: Bioinformation Source Type: journals

Extract-SAGE: An integrated platform for cross-analysis and GA-based selection of SAGE data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Serial analysis of gene expression (SAGE) is a powerful quantification technique for gene expression data. The huge amount of tag data in SAGE libraries of samples is difficult to analyze with current SAGE analysis tools. Data is often not provided in a biologically significant way for cross-analysis and -comparison, thus limiting its application. Hence, an integrated software platform that can perform such a complex task is required. Here, we implement set theory for cross-analyzing gene expression data among different SAGE libraries of tissue sources; up- or down-regulated tissue-specific tags can be identified compu...
Source: Bioinformation - March 23, 2009 Category: Bioinformatics Authors: Yang CH, Shih1 TM, Hung YC, Chang HW, Chuang LY Tags: Bioinformation Source Type: journals

ScanMoment: a web server for combinatorial analysis of basic residues in nucleic acid binding sites.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
ScanMoment is a webserver designed to identify the presence of the basic faced alpha-helix (BFAH) motif in the nucleic acid binding sites of proteins. The program calculates the 'Basic Moment', a parameter that quantitizes the distribution of basic residues on the surface of an alpha-helix. A sliding window is used to generate a plot displaying regions of the protein sequence that possesses a high Basic Moment and hus likely to possess a BFAH motif. The user may vary the periodicity from that of an alpha-helix (100 degrees ), to those of other secondary structures such as beta sheets and 3(10) helices. The program can ...
Source: Bioinformation - March 23, 2009 Category: Bioinformatics Authors: Massey SE Tags: Bioinformation Source Type: journals

RICHEST - a web server for richness estimation in biological data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Richness is defined as the number of distinct species or classes in a sample or population. Although richness estimation is an important practice, it requires mathematical and computational methods that are challenging to understand and implement. We have developed a web server, RICHness ESTimator (RICHEST), which implements three non-parametric statistical methods for richness estimation. Its user-friendly web interface allows users to analyze and compare their data conveniently over the web. AVAILABILITY: A web server hosting RICHEST is accessible at http://richest.cgb.indiana.edu/cgi-bin/index.cgi and the software i...
Source: Bioinformation - March 23, 2009 Category: Bioinformatics Authors: Durden C, Dong Q Tags: Bioinformation Source Type: journals

CHPVDB - a sequence annotation database for Chandipura Virus.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We describe herein the creation of CHPVDB, a new database that integrates information of different proteins in to a single resource. For basic curation of protein information, the database relies on features from other selected databases, servers and published reports. This database facilitates significant relationship between molecular analysis, cleavage sites, possible protein functional families assigned to different proteins of Chandipura virus (CHPV) by SVMProt and related tools. AVAILABILITY: The database is freely available at http://chpvdb.biomedinformri.org/. PMID: 19293996 [PubMed - in process] (Source: Bioinformation)
Source: Bioinformation - March 23, 2009 Category: Bioinformatics Authors: Dikhit MR, Rana SP, Das P, Sahoo GC Tags: Bioinformation Source Type: journals

Docking study of triphenylphosphonium cations as estrogen receptor alpha modulators.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Virtual high throughput screening (VHTS) was performed to assess possible interactions which might occur between commercially available triphenylphosphonium (TPP) cations and estrogen receptor alpha (ERalpha) that could be exploited to design novel ERalpha modulators. One application of TPP cations is for delivering bioactive molecules to targets in mitochondria as the large membrane potential of mitochondria leads cations to accumulate inside them. The estrogen receptors (ERs) alpha and beta, normally activated by the endogenous hormone 17beta-estradiol, are responsible for controlling transcription of nuclear DNA nec...
Source: Bioinformation - March 23, 2009 Category: Bioinformatics Authors: Salisbury JP, Williams JC Tags: Bioinformation Source Type: journals

Insights from Streptococcus pneumoniae glucose kinase structural model.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Streptococcus pneumonia is the common cause of sepsis and meningitis. Emergence of multiple antibiotic resistant strains in the community-acquired bacterium is catastrophic. Glucose kinase (GLK) is a regulatory enzyme capable of adding phosphate group to glucose in the first step of streptomycin biosynthesis. The activity of glucose kinase was regulated by the Carbon Catabolite Repression (CCR) system. Therefore, it is important to establish the structure-function relation of GLK in S. pneumoniae. However, a solved structure for S. pneumoniae GLK is not available at the protein data bank (PDB). Therefore, we created a ...
Source: Bioinformation - March 23, 2009 Category: Bioinformatics Authors: Mulakayala C, Banaganapalli BN, Anuradha C, Chitta SK Tags: Bioinformation Source Type: journals

Evaluation of optimization techniques for variable selection in logistic regression applied to diagnosis of myocardial infarction.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Logistic regression is often used to help make medical decisions with binary outcomes. Here we evaluate the use of several methods for selection of variables in logistic regression. We use a large dataset to predict the diagnosis of myocardial infarction in patients reporting to an emergency room with chest pain. Our results indicate that some of the examined methods are well suited for variable selection in logistic regression and that our model, and our myocardial infarction risk calculator, can be an additional tool to aid physicians in myocardial infarction diagnosis. PMID: 19293999 [PubMed - in process] (Source: Bioinformation)
Source: Bioinformation - March 23, 2009 Category: Bioinformatics Authors: Kiezun A, Lee IT, Shomron N Tags: Bioinformation Source Type: journals

Use of sequence motifs as barcodes and secondary structures of Internal Transcribed spacer 2 (ITS2, rDNA) for identification of the Indian liver fluke, Fasciola (Trematoda: Fasciolidae).Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics that give "morphological" information which is not found in the primary sequence. Also DNA sequence motifs from the internal transcribed spacer (ITS) of the nuclear rRNA repeat are useful for identification of trematodes. The species of liver flukes of the genus Fasciola (Platyhelminthes: Digenea: Fasciolidae) are obligate parasitic trematodes residing in the large biliary ducts of herbivorous mammals. While Fascio...
Source: Bioinformation - March 23, 2009 Category: Bioinformatics Authors: Prasad P, Tandon V, Biswal D, Goswami L, Chatterjee A Tags: Bioinformation Source Type: journals

Homology modeling of phosphoryl thymidine kinase of enterohemorrhagic Escherichia coli OH: 157.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, phosphoryl thymidine kinase (thi E), a terminal enzyme in the thiamine biosynthesis pathway in the pathogen has been modeled to be used in future as a potential drug target by the design of suitable inhibitors. PMID: 19255642 [PubMed - in process] (Source: Bioinformation)
Source: Bioinformation - March 5, 2009 Category: Bioinformatics Authors: Kaistha SD, Sinha R Tags: Bioinformation Source Type: journals

Analysis of the impact of ERK5, JNK, and P38 kinase cascades on each other: A systems approach.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The classical concept of linear pathways is being increasingly challenged by network representations, which emphasize the importance of interactions between components of a biological system, and motivates for adopting a system-level approach in biology. We have developed a dynamical system that integrates quantitative, dynamic and topological representation of network of ERK5 (Extracellular signal-regulated kinases 5), JNK(c-Jun N-terminal kinases) and P38 kinase cascades. We have observered that, the transient activation of ERK5, JNK1 and P38beta kinase, and the persistent activation of JNK2, JNK3 and P38 delta kinas...
Source: Bioinformation - March 5, 2009 Category: Bioinformatics Authors: Sundaramurthy P, Gakkhar S, Sowdhamini R Tags: Bioinformation Source Type: journals

Computational prediction and analysis of impact of the cross-talks between JNK and P38 kinase cascades.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Signal transduction is a complex protein signaling process with a rich network of multifunctional interactions that occur in a non-linear fashion. Mitogen-activated protein kinase (MAPK) signal transduction pathways regulate diverse cellular processes ranging from proliferation and differentiation to apoptosis. In mammals, out of five, there are three well characterized subfamilies of MAPKs - ERKs (Extracellular signal-regulated kinases), JNKs (c-Jun N-terminal kinases), and P38 kinases, and their activators, are implicated in human diseases and are targets for drug development. Kinase cascades in MAPK pathways mediate...
Source: Bioinformation - March 5, 2009 Category: Bioinformatics Authors: Sundaramurthy P, Gakkhar S, Sowdhamini R Tags: Bioinformation Source Type: journals

Computational screening of molecular targets in Plasmodium for novel non resistant anti-malarial drugs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Histone acetyltransferase (HAT) is an enzyme required for chromatin remodeling and transcriptional activation. Sarcoendoplasmic reticulum Ca(2+) ATPase (SERCA) is an ATP coupled Ca(2+) ion pump involved in metabolic arrest. Both these enzymes are present in Plasmodia and have been selected as molecular targets for in silico studies of some new non-resistant antimalarial drugs like artemisinin, curcumin and diarylheptanoids along with some other inhibitors reported in literature. Ten top inhibitors have also been generated based on common pharmacophore from ZINC database. The HAT enzyme was modeled with the help of the ...
Source: Bioinformation - March 5, 2009 Category: Bioinformatics Authors: Singh N, Misra K Tags: Bioinformation Source Type: journals

New tips for structure prediction by comparative modeling.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Comparative modelling is utilized to predict the 3-dimensional conformation of a given protein (target) based on its sequence alignment to experimentally determined protein structure (template). The use of such technique is already rewarding and increasingly widespread in biological research and drug development. The accuracy of the predictions as commonly accepted depends on the score of sequence identity of the target protein to the template. To assess the relationship between sequence identity and model quality, we carried out an analysis of a set of 4753 sequence and structure alignments. Throughout this research, ...
Source: Bioinformation - March 5, 2009 Category: Bioinformatics Authors: Rayan A Tags: Bioinformation Source Type: journals

Functional group based Ligand binding affinity scoring function at atomic environmental level.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Use of knowledge based scoring function (KBSF) for virtual screening and molecular docking has become an established method for drug discovery. Lack of a precise and reliable free energy function that describes several interactions including water-mediated atomic interaction between amino-acid residues and ligand makes distance based statistical measure as the only alternative. Till now all the distance based scoring functions in KBSF arena use atom singularity concept, which neglects the environmental effect of the atom under consideration. We have developed a novel knowledge-based statistical energy function for prot...
Source: Bioinformation - March 5, 2009 Category: Bioinformatics Authors: Varadwaj PK, Lahiri T Tags: Bioinformation Source Type: journals

Leaving out control groups: an internal contrast analysis of gene expression profiles in atrial fibrillation patients - A systems biology approach to clinical categorization.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Atrial fibrillation (AF) is a frequent chronic dysrythmia with an incidence that increases with age (>40). Because of its medical and socio-economic impacts it is expected to become an increasing burden on most health care systems. AF is a multi-factorial disease for which the identification of subtypes is warranted. Novel approaches based on the broad concepts of systems biology may overcome the blurred notion of normal and pathological phenotype, which is inherent to high throughput molecular arrays analysis. Here we apply an internal contrast algorithm on AF patient data with an analytical focus on potential entr...
Source: Bioinformation - March 5, 2009 Category: Bioinformatics Authors: Vanhoutte K, de Asmundis C, Francesconi A, Figys1 J, Steurs G, Boussy T, Roos M, Mueller A, Massimo L, Paparella G, Van Caelenberg K, Chierchia GB, Sarkozy A, Y Terradellas PB, Zizi M Tags: Bioinformation Source Type: journals

Genome-wide analyses of rice root development QTLs and development of an online resource, Rootbrowse.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Genetic control of root development in rice is complex and the underlying mechanisms (constitutive and adaptive) are poorly understood. Lowland and upland varieties of indica and japonica rice with contrasting root development characteristics have been crossed, mapping populations developed and a number of QTLs in different chromosomes were identified. As these studies have used different sets of markers and many of the QTLs identified are long, it is difficult to exploit the varietal difference for improved root traits by marker assisted selection and for identification of concerned alleles. Intensive data mining of l...
Source: Bioinformation - March 5, 2009 Category: Bioinformatics Authors: Suryapriya P, Snehalatha A, Kayalvili U, Krishna R, Singh S, Ulaganathan K Tags: Bioinformation Source Type: journals

WebSat - A web software for microsatellite marker development.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Simple sequence repeats (SSR), also known as microsatellites, have been extensively used as molecular markers due to their abundance and high degree of polymorphism. We have developed a simple to use web software, called WebSat, for microsatellite molecular marker prediction and development. WebSat is accessible through the Internet, requiring no program installation. Although a web solution, it makes use of Ajax techniques, providing a rich, responsive user interface. WebSat allows the submission of sequences, visualization of microsatellites and the design of primers suitable for their amplification. The program allo...
Source: Bioinformation - March 5, 2009 Category: Bioinformatics Authors: Martins WS, Soares Lucas DC, de Souza Neves KF, Bertioli DJ Tags: Bioinformation Source Type: journals

Techniques for integrating -omics data.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
The challenge for -omics research is to tackle the problem of fragmentation of knowledge by integrating several sources of heterogeneous information into a coherent entity. It is widely recognized that successful data integration is one of the keys to improve productivity for stored data. Through proper data integration tools and algorithms, researchers may correlate relationships that enable them to make better and faster decisions. The need for data integration is essential for present -omics community, because -omics data is currently spread world wide in wide variety of formats. These formats can be integrated and ...
Source: Bioinformation - March 5, 2009 Category: Bioinformatics Authors: Akula SP, Miriyala RN, Thota H, Rao AA, Gedela S Tags: Bioinformation Source Type: journals