DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment

Bioinformatics - Tập 28 Số 15 - Trang 2074-2075 - 2012
Andrea Volkamer1, Daniel Kühn1, Friedrich Rippmann1, Matthias Rarey1
11 Center for Bioinformatics, University of Hamburg, Bundesstr and 2Merck KGaA, Merck Serono, Global Computational Chemistry, Frankfurter Str. 250, 64293 Darmstadt, Germany

Tóm tắt

Abstract Motivation: Many drug discovery projects fail because the underlying target is finally found to be undruggable. Progress in structure elucidation of proteins now opens up a route to automatic structure-based target assessment. DoGSiteScorer is a newly developed automatic tool combining pocket prediction, characterization and druggability estimation and is now available through a web server. Availability: The DoGSiteScorer web server is freely available for academic use at http://dogsite.zbh.uni-hamburg.de Contact:  [email protected].

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Tài liệu tham khảo

Brylinski, 2008, A threading-based method (findsite) for ligand-binding site prediction and functional annotation, Proc. Natl. Acad. Sci. USA, 105, 129, 10.1073/pnas.0707684105

Halgren, 2009, Identifying and characterizing binding sites and assessing druggability, J. Chem. Inf. Model., 49, 377, 10.1021/ci800324m

Konc, 2010, Probis: a web server for detection of structurally similar protein binding sites, Nucleic Acids Res., 38, W436, 10.1093/nar/gkq479

Lin, 2012, Sitecomp: a server for ligand binding site analysis in protein structures, Bioinformatics (Oxford, England)., 28, 1172, 10.1093/bioinformatics/bts095

Schmidtke, 2010, Understanding and predicting druggability. a high-throughput method for detection of drug binding sites, J. Med. Chem., 53, 5858, 10.1021/jm100574m

Schmidtke, 2010, fpocket: online tools for protein ensemble pocket detection and tracking, Nucleic Acids Res., 38, W582, 10.1093/nar/gkq383

Sheridan, 2010, Drug-like density: a method of quantifying the ‘bindability’ of a protein target based on a very large set of pockets and drug-like ligands from the protein data bank, J. Chem. Inf. Model., 50, 2029, 10.1021/ci100312t

Tseng, 2009, Splitpocket: identification of protein functional surfaces and characterization of their spatial patterns, Nucleic Acids Res., 37, W384, 10.1093/nar/gkp308

Tseng, 2010, fpop: footprinting functional pockets of proteins by comparative spatial patterns, Nucleic Acids Res., 38, D288, 10.1093/nar/gkp900

Volkamer, 2010, Analyzing the topology of active sites: on the prediction of pockets and subpockets, J. Chem. Inf. Model., 50, 2041, 10.1021/ci100241y

Volkamer, 2012, Combining global and local measures for structure-based druggability predictions, J. Chem. Inf. Model., 52, 360, 10.1021/ci200454v