Benchmarking Sets for Molecular Docking Export

@article{citeulike:913782, abstract = {PMID: 17154509 Ligand enrichment among top-ranking hits is a key metric of molecular docking. To avoid bias, decoys should resemble ligands physically, so that enrichment is not simply a separation of gross features, yet be chemically distinct from them, so that they are unlikely to be binders. We have assembled a directory of useful decoys (DUD), with 2950 ligands for 40 different targets. Every ligand has 36 decoy molecules that are physically similar but topologically distinct, leading to a database of 98 266 compounds. For most targets, enrichment was at least half a log better with uncorrected databases such as the MDDR than with DUD, evidence of bias in the former. These calculations also allowed 40 40 cross-docking, where the enrichments of each ligand set could be compared for all 40 targets, enabling a specificity metric for the docking screens. DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/.}, author = {Huang, Niu and Shoichet, Brian K. and Irwin, John J.}, citeulike-article-id = {913782}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/jm0608356}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/jm0608356}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17154509}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17154509}, day = {1}, doi = {10.1021/jm0608356}, journal = {Journal of Medicinal Chemistry}, keywords = {docking, docking\_design, library, potential\_app}, month = {November}, number = {23}, pages = {6789--6801}, posted-at = {2006-10-26 18:11:12}, priority = {2}, title = {Benchmarking Sets for Molecular Docking}, url = {http://dx.doi.org/10.1021/jm0608356}, volume = {49}, year = {2006} }

TY - JOUR ID - citeulike:913782 L3 - citeulike-article-id:913782 N2 - PMID: 17154509 Ligand enrichment among top-ranking hits is a key metric of molecular docking. To avoid bias, decoys should resemble ligands physically, so that enrichment is not simply a separation of gross features, yet be chemically distinct from them, so that they are unlikely to be binders. We have assembled a directory of useful decoys (DUD), with 2950 ligands for 40 different targets. Every ligand has 36 decoy molecules that are physically similar but topologically distinct, leading to a database of 98 266 compounds. For most targets, enrichment was at least half a log better with uncorrected databases such as the MDDR than with DUD, evidence of bias in the former. These calculations also allowed 40 40 cross-docking, where the enrichments of each ligand set could be compared for all 40 targets, enabling a specificity metric for the docking screens. DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/. IS - 23 JF - Journal of Medicinal Chemistry EP - 6801 TI - Benchmarking Sets for Molecular Docking VL - 49 SP - 6789 KW - docking KW - docking_design KW - library KW - potential_app AU - Huang, Niu AU - Shoichet, Brian AU - Irwin, John PY - 2006/11/01/ UR - http://dx.doi.org/10.1021/jm0608356 ER -