Computer medicine screening method based on BFGS algorithm

A screening method and computer technology, applied in bioinformatics, used to analyze two-dimensional or three-dimensional molecular structures, instruments, etc., can solve the problem of unreasonable binding between receptors and ligands, long molecular docking time, and low screening efficiency. and other problems, to achieve the effect of reducing the cost of drug screening, small molecular weight, increasing effect and efficiency

Pending Publication Date: 2019-11-15
QINGDAO NAT LAB FOR MARINE SCI & TECH DEV CENT +1
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Problems solved by technology

[0004] The invention provides a computer drug screening method based on the BFGS algorithm, which solves the problem of low screening efficiency and screening effect caused by the long time of molecular docking and the unreasonable binding mode between receptors and ligands in the computer virtual screening method in the prior art bad question

Method used

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Embodiment 1

[0027] A kind of computer drug screening method based on BFGS algorithm of the present invention comprises the following steps:

[0028] 1) Establishing a database, the database is a data cluster established by 30,000 marine small molecules, and the marine small molecules in the data cluster are cycled through and matched to form a small molecule library with a similarity of 0-1;

[0029] 2) database preprocessing, delete the small molecule conformation with a similarity of 1 in the small molecule library obtained in step 1), and update the small molecule library;

[0030] 3) Molecular docking, take a receptor from the protein database, take multiple ligands from the updated small molecule library obtained in step 2), place the ligand at the active site of the receptor, and make multiple ligands and One receptor for molecular docking;

[0031] 4) Conformation search, use the BFGS algorithm for conformation search, match the newly generated conformation with the initial confor...

Embodiment 2

[0034] A kind of computer drug screening method based on BFGS algorithm of the present invention comprises the following steps:

[0035] 1) Establishing a database, the database is a data cluster established by 40,000 marine small molecules, and the marine small molecules in the data cluster are cyclically traversed and matched by a pairwise matching method to form a small molecule library with a similarity of 0-1, The calculation method of similarity is molecular fingerprint calculation method;

[0036] 2) database preprocessing, delete the small molecule conformation with a similarity of 1 in the small molecule library obtained in step 1), and update the small molecule library;

[0037] 3) Molecular docking, take a receptor from the protein database, take multiple ligands from the updated small molecule library obtained in step 2), place the ligand at the active site of the receptor, and make multiple ligands and Molecular docking of one receptor, the method of molecular dock...

Embodiment 3

[0041] A kind of computer drug screening method based on BFGS algorithm of the present invention comprises the following steps:

[0042] 1) Establish a database. The database is a data cluster established by 35,000 marine small molecules with a relative molecular weight less than 500. The marine small molecules in the data cluster are cyclically traversed and matched by a pairwise matching method to form a similarity of 0.85-1 The small molecule library, the calculation method of similarity is molecular fingerprint calculation method;

[0043] 2) database preprocessing, delete the small molecule conformation with a similarity of 1 in the small molecule library obtained in step 1), and update the small molecule library;

[0044] 3) Molecular docking, take a receptor from the protein database, take multiple ligands from the updated small molecule library obtained in step 2), place the ligand at the active site of the receptor, and make multiple ligands and A receptor for molecu...

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Abstract

The invention discloses a computer medicine screening method based on a BFGS algorithm. The method comprises the following steps of 1) database establishment, wherein a data set cluster composed of 30,000-40,000 marine micromolecules is subjected to searching loop matching to form a micromolecule library with the similarity of 0-1; 2) database pre-processing, wherein micromolecule conformations, with the similarity of 1, in the micromolecule library obtained in step 1) are deleted; 3) molecular docking, wherein ligands are placed at active loci of a receptor, so that multiple ligands and one receptor are in molecular docking; 4) searching for conformations, wherein the BFGS algorithm is used for searching for the conformations, and when newly-generated conformations are identical to initial conformations or preset difference values of the newly-generated conformations and the initial conformations are smaller than or equal to 0.0001, searching for the conformations is stopped. According to the computer medicine screening method, by optimizing the algorithm, the time of searching for the low-energy conformations of the ligands and the receptor which are combined at the active loci of the receptor in the algorithm is shortened, and the effect and efficiency of virtual screening of a micromolecule database based on the method are improved.

Description

technical field [0001] The invention belongs to the technical field of computer-aided drug design, in particular to a computer drug screening method based on BFGS algorithm. Background technique [0002] Drug screening refers to the process of evaluating the biological activity, pharmacological effect and medicinal value of substances (sampling) that may be used as drugs by using appropriate methods. Drug screening is screening at the biochemical and cellular levels. With the update of computer technology and the development of big data technology, the application of virtual screening strategy for drug screening has gradually become the mainstream. Virtual screening, that is, before the biological activity screening, use the molecular docking software on the computer to simulate the interaction between the target target and the candidate drug, and calculate the affinity between the two, so as to reduce the number of actual screening compounds and increase the lead. Compoun...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B15/30
CPCG16B15/30
Inventor 魏志强刘素娥刘昊徐锡明杨金波汪雪婷
Owner QINGDAO NAT LAB FOR MARINE SCI & TECH DEV CENT
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