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CoPub: a literature-based keyword enrichment tool for microarray data analysis
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.
Comparison between steroid binding to membrane progesterone receptor α (mPRα) and to nuclear progesterone receptor: Correlation with physicochemical properties assessed by comparative molecular field…
Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases
- Raoul Frijters, M. Vugt, R. Smeets, R. V. Schaik, J. D. Vlieg, W. Alkema
- BiologyPLoS Comput. Biol.
- 1 September 2010
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.
Pharmacophore Fingerprint-Based Approach to Binding Site Subpocket Similarity and Its Application to Bioisostere Replacement
- David J. Wood, J. D. Vlieg, M. Wagener, T. Ritschel
- Chemistry, BiologyJ. Chem. Inf. Model.
- 16 August 2012
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.
CoPub update: CoPub 5.0 a text mining system to answer biological questions
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.
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood
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.
Comparative Analysis of Pharmacophore Screening Tools
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.
Snooker: A Structure-Based Pharmacophore Generation Tool Applied to Class A GPCRs
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.
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)…
PhyloPat: phylogenetic pattern analysis of eukaryotic genes
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.