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A method for protein ATP docking based on differential evolution

A differential evolution, protein technology, applied to the analysis of two-dimensional or three-dimensional molecular structures, instruments, artificial life, etc.

Active Publication Date: 2021-04-06
ZHEJIANG UNIV OF TECH
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Problems solved by technology

[0006] Therefore, the existing protein ATP molecular docking methods have shortcomings in terms of computational cost and search efficiency, and need to be improved

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  • A method for protein ATP docking based on differential evolution
  • A method for protein ATP docking based on differential evolution
  • A method for protein ATP docking based on differential evolution

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Embodiment Construction

[0044] The present invention will be further described below in conjunction with the accompanying drawings.

[0045] refer to figure 1 and figure 2 , a method for docking proteins and ATP based on differential evolution, comprising the following steps:

[0046] 1) Input the structural information of protein and ATP, denoted as R and A respectively;

[0047] 2) For the input structure information R, use the ATPbind server (https: / / zhanglab.ccmb.med.umich.edu / ATPbind / ) to predict the residue site information of protein-ATP binding, and obtain the protein-ATP binding residue site information The given n residues are denoted as r 1 ,r 2 ,...,r n ;

[0048] 3) According to r 1 ,r 2 ,...,r n The central carbon atom C α Coordinate information clusters a center point C R , according to the coordinate information of each atom in A, a center point C is clustered A , moving ATP such that C A and C R The coordinates of these two points coincide;

[0049] 4) According to th...

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Abstract

A differential evolution-based protein ATP docking method. First, the ATPbind server is used to predict the protein-ATP binding residue information, which improves the prediction accuracy of the molecular spatial structure of the complex; then, the original protein-ATP is designed by population individuals. The ATP structure prediction problem is transformed into an optimization problem of searching for the optimal individual, which reduces the computational cost. Finally, by using the differential evolution algorithm to search for the optimal individual, the prediction accuracy of the protein-ATP complex structure is improved. The invention provides a protein ATP docking method based on differential evolution with low computational cost and high search efficiency.

Description

technical field [0001] The invention relates to the fields of bioinformatics, intelligent optimization and computer application, and in particular to a protein ATP docking method based on differential evolution. Background technique [0002] With the continuous and in-depth research on proteins, it is found that the phenomenon of protein binding to small molecules or ligands is ubiquitous, especially the combination of proteins and energy molecules is widely present in various life phenomena. Therefore, the research on the binding of proteins and ligands Characteristics and laws are very necessary. ATP is an unstable high-energy compound, also known as adenosine triphosphate. It releases more energy during hydrolysis, which is the most direct energy source in organisms. In cells, it can convert with ADP to realize energy storage and release, thus ensuring the energy supply for various life activities of cells. Many important physiological processes in organisms, such as c...

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B15/30G16B40/00G06N3/00
CPCG06N3/006G16B15/30G16B40/00
Inventor 饶亮张贵军刘俊彭春祥胡俊周晓根
Owner ZHEJIANG UNIV OF TECH
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