LigDockCSA protein-ligand docking using conformational space annealing

LigDockCSA : protein-ligand docking using conformational space annealing

Copyright © 2011 Wiley Periodicals, Inc.

Bibliographische Detailangaben
Veröffentlicht in:Journal of computational chemistry. - 1984. - 32(2011), 15 vom: 30. Nov., Seite 3226-32
1. Verfasser: Shin, Woong-Hee (VerfasserIn)
Weitere Verfasser: Heo, Lim, Lee, Juyong, Ko, Junsu, Seok, Chaok, Lee, Jooyoung
Format: Online-Aufsatz
Sprache:English
Veröffentlicht: 2011
Zugriff auf das übergeordnete Werk:Journal of computational chemistry
Schlagworte:Evaluation Study Journal Article Research Support, Non-U.S. Gov't Ligands Proteins
Beschreibung
Zusammenfassung:Copyright © 2011 Wiley Periodicals, Inc.
Protein-ligand docking techniques are one of the essential tools for structure-based drug design. Two major components of a successful docking program are an efficient search method and an accurate scoring function. In this work, a new docking method called LigDockCSA is developed by using a powerful global optimization technique, conformational space annealing (CSA), and a scoring function that combines the AutoDock energy and the piecewise linear potential (PLP) torsion energy. It is shown that the CSA search method can find lower energy binding poses than the Lamarckian genetic algorithm of AutoDock. However, lower-energy solutions CSA produced with the AutoDock energy were often less native-like. The loophole in the AutoDock energy was fixed by adding a torsional energy term, and the CSA search on the refined energy function is shown to improve the docking performance. The performance of LigDockCSA was tested on the Astex diverse set which consists of 85 protein-ligand complexes. LigDockCSA finds the best scoring poses within 2 Å root-mean-square deviation (RMSD) from the native structures for 84.7% of the test cases, compared to 81.7% for AutoDock and 80.5% for GOLD. The results improve further to 89.4% by incorporating the conformational entropy
Beschreibung:Date Completed 21.02.2012
Date Revised 10.12.2019
published: Print-Electronic
Citation Status MEDLINE
ISSN:1096-987X
DOI:10.1002/jcc.21905