期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 37, 期 18, 页码 1734-1739出版社
WILEY-BLACKWELL
DOI: 10.1002/jcc.24380
关键词
virtual screening; structure-based drug discovery; structural similarity; ligand similarity
资金
- National Health and Medical Research Council of Australia [1059775, 1083450]
- Australian Research Council's Linkage Infrastructure, Equipment and Facilities [LE150100161]
- National Natural Science Foundation of China [61271378]
Structure-based virtual screening usually involves docking of a library of chemical compounds onto the functional pocket of the target receptor so as to discover novel classes of ligands. However, the overall success rate remains low and screening a large library is computationally intensive. An alternative to this ab initio approach is virtual screening by binding homology search. In this approach, potential ligands are predicted based on similar interaction pairs (similarity in receptors and ligands). SPOT-Ligand is an approach that integrates ligand similarity by Tanimoto coefficient and receptor similarity by protein structure alignment program SPalign. The method was found to yield a consistent performance in DUD and DUD-E docking benchmarks even if model structures were employed. It improves over docking methods (DOCK6 and AUTODOCK Vina) and has a performance comparable to or better than other binding-homology methods (FINDsite and PoLi) with higher computational efficiency. The server is available at http://sparks-lab.org. (C) 2016 Wiley Periodicals, Inc.
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