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Docking method for proteins, water molecules and ligands

A water molecule and protein technology, applied in molecular design, multi-objective optimization, design optimization/simulation, etc., can solve problems such as high computational complexity, easy to fall into local minimum, etc., to improve search performance, avoid repeated parameter debugging, The effect of increasing quantity and variety

Pending Publication Date: 2020-02-11
SHANGHAI DIANJI UNIV
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Problems solved by technology

However, this kind of method still has high computational complexity and is easy to fall into the defects of local minimum.
Therefore, such methods are not suitable for virtual screening of compound libraries, especially large-scale compound libraries.

Method used

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  • Docking method for proteins, water molecules and ligands
  • Docking method for proteins, water molecules and ligands
  • Docking method for proteins, water molecules and ligands

Examples

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Embodiment

[0059] This example provides a docking method suitable for proteins, water molecules and ligands with an uncertain number of molecules, which can avoid falling into a local optimum and has low computational complexity, such as figure 1 shown, including the following steps:

[0060] Step S1: Establish a multi-target docking model;

[0061] Step S2: optimize the multi-objective docking model through the genetic algorithm based on the combination of adaptive operators, unequal length chromosomes and elite individual selection, and obtain the optimal docking solution;

[0062] Step S3: Based on the optimal docking solution, the docking of proteins, water molecules and ligands is carried out.

[0063] in particular:

[0064] 1) Adaptive operator

[0065] For the two important control parameters of the genetic algorithm, the crossover probability and the mutation probability, let them participate in the entire evolution process as optimal design variables, so that the changes of ...

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Abstract

The invention relates to a docking method for proteins, water molecules and ligands. The method comprises the steps that S1 a multi-target docking model is established; S2 a genetic algorithm based onthe combination of an adaptive operator, unequal long chromosomes and elite individual selection is used to optimize the multi-target docking model to acquire the optimal docking solution; and S3 based on the docking optimal solution, docking of proteins, water molecules and ligands is carried out. Compared with the prior art, the docking method has the advantages that repeated parameter debugging is avoided, thereby reducing the computational complexity; the problem of uncertain number of water molecules in the multi-body docking process is solved; population is prevented from falling into alocal optimum; and the search performance of the algorithm is improved.

Description

technical field [0001] The invention relates to the field of drug design, in particular to a docking method of proteins, water molecules and ligands. Background technique [0002] Traditional molecular docking methods mostly consider water molecules implicitly or explicitly by ignoring water molecules, or considering them as part of the receptor and only considering their resting states. Although these strategies can simplify the calculation model to varying degrees and reduce the computational complexity, they all have an impact on the accuracy of the prediction of the receptor-ligand binding mode and the calculation of the binding affinity between the two. In the process of docking between proteins and ligands, multiple factors such as the quantity change or dynamic movement of water molecules participating in the interaction can be considered comprehensively, and then the real binding process can be approximated. [0003] The multibody docking methods that consider the p...

Claims

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Application Information

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IPC IPC(8): G16C20/50G06F30/20G06F111/06
CPCG16C20/50
Inventor 肖薇
Owner SHANGHAI DIANJI UNIV
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