Device and method for optimizing stretching direction in stretching molecular kinetics simulation

Abstract

The invention provides a method for optimizing the stretching direction in the stretching molecular dynamics, which provides support for analysis of interaction of a ligand and a receptor, conformation variation of ligand induced proteins, selective combination of the ligand and the receptor and determination of an optimum combination path. Firstly, the stretching direction which is selected initially is judged, and optimization of the direction begins only when the tension reaches a certain threshold; secondly, search and optimization of the stretching direction in a three-dimensional space are performed according to the information entropy based multi-population genetic algorithm, and a novel stretching direction after optimization is obtained; thirdly, the prior two steps are cycled until stretching simulation is ended. A reasonable stretching direction is searched in the stretching molecular dynamics simulation process through optimization of the stretching direction, thereby the mode in the prior stretching molecular dynamics simulation process that the stretching direction is unitary and unchanged is improved, and a more proper path and a more proper means are searched.

Description

technical field [0001] The invention relates to a method and device for optimizing the stretching direction in stretching molecular dynamics simulation, which is suitable for analyzing the interaction between ligands and receptors, the conformational changes of ligand-induced proteins, and the selection of ligands and receptors Determination of sexual combination and optimal combination path. Background technique [0002] Molecular Dynamics Simulation (Rahman, A. and F.H. Stillinger (1971). "Molecular dynamics study of liquidwater." J Chem Phys 55(7):3336-3359) is the most widely used computational simulation method in the study of the relationship between the structure and function of biological macromolecules. Molecular dynamics simulation is to use computer to simulate the motion process of atomic nuclei in a multi-particle system composed of atomic nuclei and electrons, in which each atomic nucleus is regarded as moving according to Newton's law under the action of the...

AI Technical Summary

Problems solved by technology

Although new methods can play an active role in exploring and testing possible dissociation channels of ligand molecules, they cannot simulate processes such as ligand-induced conformational changes of receptors in a precise and continuous manner, and only rely on the subjective guesswork of researchers And artificial control is only a part of the whole stretching molecular dynamics simulation, it must be combined with traditional stretching molecular dynamics to do further detailed simulation and inspection work

These methods can only serve as an auxiliary work for the stretching molecular dynamics simulation in the early stage, and help to determine the stretching direction at the beginning of the stretching molecular dynamics simulation, but cannot replace it

Images