Coupling dihedral angle parameter optimization method based on CMAP potential function and protein force field

Abstract

The invention relates to the technical field of molecular dynamics simulation, in particular to a protein force field, and more particularly relates to a coupling dihedral angle parameter optimizationmethod based on a CMAP potential function. According to the optimization method, an existing protein force field is taken as a parent force field, local intrinsic conformation preference in a crimp library is taken as a fitting target, and dihedral angle parameters of amino acid residues in the parent force field are optimized, so that local conformation distribution obtained through molecular dynamics simulation and distribution in the crimp library reach preset similarity. The invention also relates to a protein force field obtained by the optimization method. According to the method, coupled dihedral angles in protein molecules can be simply and efficiently optimized at the same time, the dihedral angle parameter optimization process is simple, efficient and automatic, the residue specific force field RSFF2C with high compatibility is obtained, and the method can be widely applied to various kinds of MD software.

Description

technical field [0001] The invention relates to the technical field of molecular dynamics simulation, in particular to a protein force field, and more specifically to a coupling dihedral angle parameter optimization method based on a CMAP potential function and the resulting protein force field. Background technique [0002] As the main bearer of life activities in cells, protein has always been an important research object in life science and related disciplines. The research on proteins is mainly carried out around the basic paradigm of "sequence-structure-function", among which the structure of proteins is especially the focus, because the spatial structure of proteins can help people better understand their functions from the microscopic level, and then provide protein engineering and Researches such as drug design and screening provide an important basis. At present, thanks to the development and popularization of gene sequencing technology, protein sequence databases ...

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Problems solved by technology

[0012] Aiming at the problems of complex parameterization and poor compatibility in the existing RSFF force field, inspired by the CHARMM force field, the present invention proposes a coupling dihedral angle parameter optimization method based on CMAP potential function, and then obtains an optimized protein force field

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