Blind docking of pharmaceutically relevant compounds using RosettaLigand Export

@article{citeulike:5054274, abstract = {It is difficult to properly validate algorithms that dock a small molecule ligand into its protein receptor using data from the public domain: the predictions are not blind because the correct binding mode is already known, and public test cases may not be representative of compounds of interest such as drug leads. Here, we use private data from a real drug discovery program to carry out a blind evaluation of the RosettaLigand docking methodology and find that its performance is on average comparable with that of the best commercially available current small molecule docking programs. The strength of RosettaLigand is the use of the Rosetta sampling methodology to simultaneously optimize protein sidechain, protein backbone and ligand degrees of freedom; the extensive benchmark test described here identifies shortcomings in other aspects of the protocol and suggests clear routes to improving the method.}, address = {Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350; GlaxoSmithKline Pharmaceuticals, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426; Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195-7350}, author = {Davis, Ian W. and Raha, Kaushik and Head, Martha S. and Baker, David}, citeulike-article-id = {5054274}, citeulike-linkout-0 = {http://dx.doi.org/10.1002/pro.192}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19554568}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19554568}, citeulike-linkout-3 = {http://www3.interscience.wiley.com/cgi-bin/abstract/122465391/ABSTRACT}, day = {24}, doi = {10.1002/pro.192}, issn = {1469-896X}, journal = {Protein Science}, keywords = {docking, ligand-protein-binding}, month = {June}, number = {9}, pages = {1998--2002}, posted-at = {2009-07-04 08:48:01}, priority = {2}, title = {Blind docking of pharmaceutically relevant compounds using RosettaLigand}, url = {http://dx.doi.org/10.1002/pro.192}, volume = {18}, year = {2009} }

TY - JOUR ID - citeulike:5054274 L3 - citeulike-article-id:5054274 N2 - It is difficult to properly validate algorithms that dock a small molecule ligand into its protein receptor using data from the public domain: the predictions are not blind because the correct binding mode is already known, and public test cases may not be representative of compounds of interest such as drug leads. Here, we use private data from a real drug discovery program to carry out a blind evaluation of the RosettaLigand docking methodology and find that its performance is on average comparable with that of the best commercially available current small molecule docking programs. The strength of RosettaLigand is the use of the Rosetta sampling methodology to simultaneously optimize protein sidechain, protein backbone and ligand degrees of freedom; the extensive benchmark test described here identifies shortcomings in other aspects of the protocol and suggests clear routes to improving the method. IS - 9 JF - Protein Science SN - 1469-896X AD - Department of Biochemistry, University of Washington, Seattle, Washington 98195-7350; GlaxoSmithKline Pharmaceuticals, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426; Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195-7350 EP - 2002 TI - Blind docking of pharmaceutically relevant compounds using RosettaLigand VL - 18 SP - 1998 KW - docking KW - ligand-protein-binding AU - Davis, Ian AU - Raha, Kaushik AU - Head, Martha AU - Baker, David PY - 2009/06/24/ UR - http://dx.doi.org/10.1002/pro.192 ER -