title: SPOT-Ligand: Fast and effective structure-based virtual screening by binding homology search according to ligand and receptor similarity.
abstract: 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. © 2016 Wiley Periodicals, Inc.
authors.affiliation: Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD, 4222, Australia.
authors.forename: Yuedong
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD, 4222, Australia.
authors.forename: Jian
authors.initials: J
authors.lastname: Zhan
authors.affiliation: Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Dr, Southport, QLD, 4222, Australia.
authors.forename: Yaoqi
authors.identifier: 0000-0002-9958-5699
authors.initials: Y
authors.lastname: Zhou
mesh_terms: D001665:Binding Sites; D055808:Drug Discovery; D008024:Ligands; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D040681:Structural Homology, Protein; D013997:Time Factors
chemical_list: D008024:Ligands; D011506:Proteins
keywords: ligand similarity; structural similarity; structure-based drug discovery; virtual screening