Paper Info
Title
An efficient molecular docking using conformational space annealing.
Abstract
(C) 2004 Wiley Periodicals, Inc.Molecular docking falls into the general category of global optimization problems because its main purpose is to find the most stable complex consisting of a receptor and its ligand. Conformational space annealing (CSA), a powerful global optimization method, is incorporated with the Tinker molecular modeling package to perform molecular docking simulations of six receptor-ligand complexes (3PTB, 1ULB, 2CPP, 1STP, 3CPA, and 1PPH) from the Protein Data Bank. In parallel, Monte Carlo with the minimization (MCM) method is also incorporated into the Tinker package for comparison. The energy function, consisting of electrostatic interactions, van der Waals interactions, and torsional energy terms, is calculated using the AMBER94 all-atom empirical force field. Rigid docking simulations for all six complexes and flexible docking simulations for three complexes (1STP, 3CPA, and 1PPH) are carried out using the CSA and the MCM methods. The simulation results show that the docking procedures using the CSA method generally find the most stable complexes as well as the native-like complexes more efficiently and accurately than those using the MCM, demonstrating that CSA is a promising search method for molecular docking problems.
Year
DOI
Venue
2005
10.1002/jcc.20147
JOURNAL OF COMPUTATIONAL CHEMISTRY
Keywords
Field
DocType
molecular docking,receptor-ligand complex,global optimization,conformational space annealing,Monte Carlo with minimization
Docking (molecular),Monte Carlo method,Lead Finder,Global optimization,Docking (dog),Searching the conformational space for docking,Computational chemistry,Chemistry,Protein Data Bank,Molecular model
Journal
Volume
Issue
ISSN
26
1
0192-8651
Citations 
PageRank 
References 
9
0.74
10
Authors
4
Name
Order
Citations
PageRank
Kyoungrim Lee190.74
Cezary Czaplewski24810.09
Seungyeon Kim38714.53
Jooyoung Lee49910.25