A steered molecular dynamics method with adaptive direction adjustments |
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| Authors: | Kun Yang Hualiang Jiang |
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| Affiliation: | a Department of Engineering Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology, Dalian 116024, China
b Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China |
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| Abstract: | In this paper, a new steered molecular dynamics (SMD) method with adjusting pulling direction is proposed to search an optimum trajectory of ligand dissociation. A multiobjective model and a searching technique based on information entropy with multi-population are developed to optimize the pulling direction. The improved method has been used to dissociate the substrate-bound complex structure of cytochrome P450 3A4-metyrapone. A more favorable dissociation pathway can be gained. The results show that the new pathway obtained by the proposed method has less dissociation time, smaller rupture force and lower energy barrier than that by the conventional SMD. |
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| Keywords: | Steered molecular dynamics Dissociation pathway Genetic algorithm Information entropy Metyrapone-P450 3A4 complex |
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