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Ligand Binding Site Detection b Local Structure Alignment and Its Performance Complementarity
dc.contributor.author | Lee, Hui Sun | |
dc.contributor.author | Im, Wonpil | |
dc.date.accessioned | 2017-05-17T15:01:55Z | |
dc.date.available | 2017-05-17T15:01:55Z | |
dc.date.issued | 2013-09-23 | |
dc.identifier.citation | Lee, H. S., & Im, W. (2013). Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity. Journal of Chemical Information and Modeling, 53(9), 10.1021/ci4003602. http://doi.org/10.1021/ci4003602 | en_US |
dc.identifier.uri | http://hdl.handle.net/1808/24230 | |
dc.description.abstract | Accurate determination of potential ligand binding sites (BS) is a key step for protein function characterization and structure-based drug design. Despite promising results of template-based BS prediction methods using global structure alignment (GSA), there is a room to improve the performance by properly incorporating local structure alignment (LSA) because BS are local structures and often similar for proteins with dissimilar global folds. We present a template-based ligand BS prediction method using G-LoSA, our LSA tool. A large benchmark set validation shows that G-LoSA predicts drug-like ligands’ positions in single-chain protein targets more precisely than TM-align, a GSA-based method, while the overall success rate of TM-align is better. G-LoSA is particularly efficient for accurate detection of local structures conserved across proteins with diverse global topologies. Recognizing the performance complementarity of G-LoSA to TM-align and a non-template geometry-based method, fpocket, a robust consensus scoring method, CMCS-BSP (Complementary Methods and Consensus Scoring for ligand Binding Site Prediction), is developed and shows improvement on prediction accuracy. The G-LoSA source code is freely available at http://im.bioinformatics.ku.edu/GLoSA. | en_US |
dc.publisher | American Chemical Society | en_US |
dc.rights | This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Information and Modeling, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1021/ci300178e. | en_US |
dc.subject | Template-based method | en_US |
dc.subject | G-LoSA | en_US |
dc.subject | Global structure alignment | en_US |
dc.subject | Pocket shape | en_US |
dc.subject | Computer-aided drug design | en_US |
dc.title | Ligand Binding Site Detection b Local Structure Alignment and Its Performance Complementarity | en_US |
dc.type | Article | en_US |
kusw.kuauthor | Lee, Hui Sun | |
kusw.kuauthor | Im, Wonpil | |
kusw.kudepartment | Molecular Biosciences | en_US |
dc.identifier.doi | 10.1021/ci4003602 | en_US |
kusw.oaversion | Scholarly/refereed, author accepted manuscript | en_US |
kusw.oapolicy | This item meets KU Open Access policy criteria. | en_US |
dc.identifier.pmid | PMC3821077 | en_US |
dc.rights.accessrights | openAccess |