title: An improved adaptive genetic algorithm for protein-ligand docking.
abstract: A new optimization model of molecular docking is proposed, and a fast flexible docking method based on an improved adaptive genetic algorithm is developed in this paper. The algorithm takes some advanced techniques, such as multi-population genetic strategy, entropy-based searching technique with self-adaptation and the quasi-exact penalty. A new iteration scheme in conjunction with above techniques is employed to speed up the optimization process and to ensure very rapid and steady convergence. The docking accuracy and efficiency of the method are evaluated by docking results from GOLD test data set, which contains 134 protein-ligand complexes. In over 66.2% of the complexes, the docked pose was within 2.0 A root-mean-square deviation (RMSD) of the X-ray structure. Docking time is approximately in proportion to the number of the rotatable bonds of ligands.
authors.affiliation: Department of Computer Science and Engineering, School of Electronic and Information Engineering, Dalian University of Technology, Dalian, 116023, China.
authors.forename: Ling
authors.initials: L
authors.lastname: Kang
authors.forename: Honglin
authors.initials: H
authors.lastname: Li
authors.forename: Hualiang
authors.initials: H
authors.lastname: Jiang
authors.forename: Xicheng
authors.initials: X
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D008024:Ligands; D008962:Models, Theoretical; D011506:Proteins / Q000737:chemistry*; D014961:X-Ray Diffraction
chemical_list: D008024:Ligands; D011506:Proteins
references.citation: J Comput Chem. 2005 Jan 15;26(1):78-87
references.pmid: 15538770
references.citation: J Comput Aided Mol Des. 1997 Jul;11(4):333-44
references.pmid: 9334900
references.citation: J Mol Biol. 1997 Apr 4;267(3):727-48
references.pmid: 9126849
references.citation: J Mol Biol. 1996 Aug 23;261(3):470-89
references.pmid: 8780787
references.citation: Proteins. 1993 Nov;17(3):266-78
references.pmid: 8272425
references.citation: Proteins. 1998 Nov 15;33(3):367-82
references.pmid: 9829696
references.citation: J Comput Aided Mol Des. 1996 Aug;10(4):293-304
references.pmid: 8877701
references.citation: J Comput Aided Mol Des. 1999 Sep;13(5):435-51
references.pmid: 10483527
references.citation: J Mol Biol. 1982 Oct 25;161(2):269-88
references.pmid: 7154081
references.citation: J Med Chem. 2004 Mar 25;47(7):1739-49
references.pmid: 15027865
references.citation: J Med Chem. 2000 Dec 14;43(25):4759-67
references.pmid: 11123984
references.citation: Bioinformatics. 2002 Oct;18(10):1365-73
references.pmid: 12376381
references.citation: J Med Chem. 2003 Feb 13;46(4):499-511
references.pmid: 12570372
references.citation: Proteins. 1999 Nov 1;37(2):228-41
references.pmid: 10584068
references.citation: J Comput Aided Mol Des. 2001 May;15(5):411-28
references.pmid: 11394736
references.citation: J Mol Recognit. 1996 Jan-Feb;9(1):1-5
references.pmid: 8723313