LigMatch: A Multiple Structure-Based Ligand Matching Method for 3D Virtual Screening Export

@article{citeulike:5488171, abstract = {PMID: 19685924 We have developed a new virtual screening (VS) method called LigMatch and evaluated its performance on 13 protein targets using a filtered and clustered version of the directory of useful decoys (DUD). The method uses 3D structural comparison to a crystallographically determined ligand in a bioactive 'template' conformation, using a geometric hashing method, in order to prioritize each database compound. We show that LigMatch outperforms several other widely used VS methods on the 13 DUD targets. We go on to demonstrate that improved VS performance can be gained from using multiple, structurally diverse templates rather than a single template ligand for a particular protein target. In this case, a 2D fingerprint-based method is used to select a ligand template from a set of known bioactive conformations. Furthermore, we show that LigMatch performs well even in the absence of 2D similarity to the template ligands, thereby demonstrating its robustness with respect to purely 2D methods and its potential for scaffold hopping.}, author = {Kinnings, Sarah L. and Jackson, Richard M.}, citeulike-article-id = {5488171}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/ci900204y}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/ci900204y}, doi = {10.1021/ci900204y}, journal = {Journal of Chemical Information and Modeling}, keywords = {virtual-screening}, number = {0}, posted-at = {2009-08-26 14:59:43}, priority = {2}, title = {LigMatch: A Multiple Structure-Based Ligand Matching Method for 3D Virtual Screening}, url = {http://dx.doi.org/10.1021/ci900204y}, volume = {0}, year = {0000} }

TY - JOUR ID - citeulike:5488171 L3 - citeulike-article-id:5488171 N2 - PMID: 19685924 We have developed a new virtual screening (VS) method called LigMatch and evaluated its performance on 13 protein targets using a filtered and clustered version of the directory of useful decoys (DUD). The method uses 3D structural comparison to a crystallographically determined ligand in a bioactive ‘template’ conformation, using a geometric hashing method, in order to prioritize each database compound. We show that LigMatch outperforms several other widely used VS methods on the 13 DUD targets. We go on to demonstrate that improved VS performance can be gained from using multiple, structurally diverse templates rather than a single template ligand for a particular protein target. In this case, a 2D fingerprint-based method is used to select a ligand template from a set of known bioactive conformations. Furthermore, we show that LigMatch performs well even in the absence of 2D similarity to the template ligands, thereby demonstrating its robustness with respect to purely 2D methods and its potential for scaffold hopping. IS - 0 JF - Journal of Chemical Information and Modeling TI - LigMatch: A Multiple Structure-Based Ligand Matching Method for 3D Virtual Screening VL - 0 KW - virtual-screening AU - Kinnings, Sarah AU - Jackson, Richard PY - 2000/// UR - http://dx.doi.org/10.1021/ci900204y ER -