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CoPub: a literature-based keyword enrichment tool for microarray data analysis
TLDR
A publicly available tool called CoPub that uses the information in the Medline database for the biological interpretation of microarray data, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. Expand
Comparison between steroid binding to membrane progesterone receptor α (mPRα) and to nuclear progesterone receptor: Correlation with physicochemical properties assessed by comparative molecular field
TLDR
A comparison of the CoMFA field graphs for the two receptors revealed several differences in the structural features required for binding to hu-mPRalpha and nPR which could be exploited to develop additional mPR-specific ligands. Expand
Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases
TLDR
The results show that CoPub Discovery is able to identify novel associations between genes, drugs, pathways and diseases that have a high probability of being biologically valid, making it a useful tool to unravel the mechanisms behind disease, to find novel drug targets, or to finding novel applications for existing drugs. Expand
CoPub update: CoPub 5.0 a text mining system to answer biological questions
TLDR
CoPub 5.0 is presented, a publicly available text mining system, which uses Medline abstracts to calculate robust statistics for keyword co-occurrences and provides highlighting and sorting mechanisms, using its statistics, to retrieve the most important abstracts in which the terms co-Occur. Expand
Pharmacophore Fingerprint-Based Approach to Binding Site Subpocket Similarity and Its Application to Bioisostere Replacement
TLDR
KRIPO (Key Representation of Interaction in POckets): a new method for quantifying the similarities of binding site subpockets based on pharmacophore fingerprints is presented, and potentially valuable bioisosteric replacements for all subpockets of the two studied protein are identified. Expand
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood
TLDR
This work used a single linkage clustering algorithm to create 241 697 phylogenetic lineages, using all the orthologies provided by Ensembl v49, and described an updated version of PhyloPat which can be queried by an improved web server. Expand
Comparative Analysis of Pharmacophore Screening Tools
TLDR
A comparative analysis of eight pharmacophore screening algorithms for their use in typical HTVS campaigns against four different biological targets by using default settings provides a valuable benchmark set for further developments in the field of Pharmacophore search algorithms, e.g., by using pose predictions and compound library enrichment criteria. Expand
Snooker: A Structure-Based Pharmacophore Generation Tool Applied to Class A GPCRs
TLDR
Snooker is presented, a structure-based approach to generate pharmacophore hypotheses for compounds binding to this extracellular side of the structurally conserved transmembrane domain of the GPCR protein family and it is shown that ligand poses predicted by Snooker pharmacophores reproduce literature supported binding modes for ∼75% of compounds fulfilling pharmacophile constraints. Expand
ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs
BackgroundG-protein coupled receptors (GPCRs) are involved in many different physiological processes and their function can be modulated by small molecules which bind in the transmembrane (TM)Expand
PhyloPat: phylogenetic pattern analysis of eukaryotic genes
TLDR
PhyloPat is the first tool to combine complete genome information with phylogenetic pattern querying and is presented, which allows the complete Ensembl gene database to be queried using phylogenetic patterns. Expand
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