Method for calculating and simulating protein-protein docking

A protein and protein complex technology, applied in computing, special data processing applications, instruments, etc., can solve problems such as inability to distinguish between natural and wrong binding modes, and achieve the effect of improving screening efficiency

Inactive Publication Date: 2012-01-11
LANGCHAO ELECTRONIC INFORMATION IND CO LTD
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Problems solved by technology

In many cases, however, simple geometric complementarity or molecular potential energy functions cannot discriminate between near-native and mis-binding modes.

Method used

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  • Method for calculating and simulating protein-protein docking
  • Method for calculating and simulating protein-protein docking
  • Method for calculating and simulating protein-protein docking

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Embodiment Construction

[0026] The method of the present invention is described in detail below with reference to the accompanying drawings.

[0027] A computational simulation method for protein-protein docking, the idea of ​​the present invention is as follows: We combine several different molecular docking methods, and after screening with different scoring functions, select a certain number of protein complexes, and then perform a new round of Molecular docking, the docked complexes were then subjected to cluster analysis based on structural similarity. Clustering analysis can group compounds with similar structures into one category, and we select the groups with the most conformations in the same group of complexes to use the scoring function we designed for screening. The scoring function combines the scoring function of ENDES and the scoring function of DDFIRE. The scoring function of ENDES takes into account protein structure propensity and protein evolution information. DDFIRE is a scoring...

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Abstract

The invention relates to a method for calculating and simulating protein-protein docking, which mainly comprises the following steps: downloading a protein docking benchmark database; carrying out global sampling by using macromolecular docking software, i.e. 3DDOCK, ZDOCK and ROSETTA; screening protein compounds which are obtained through sampling by using scoring functions, i.e. DOPE, RAPDF and DDFIRE, so as to filter off most of the protein compounds; carrying out second molecular docking on compounds which are obtained through screening, i.e. second sampling; clustering protein compounds which are obtained through the second sampling, and carrying out second-round screening by using the designed scoring function, i.e. Spcd, after the protein compounds are clustered; and screening more target compounds through a method of combining different docking software, multi-round docking and multiple scoring. The designed scoring function, i.e. the Spcd, can distinguish compounds in a closely-natural bonding mode from compounds in a wrong bonding mode with high efficiency, thus more target molecular compounds can be obtained, which is the most outstanding advantage of the method provided by the invention.

Description

[0001] technical field [0002] The invention relates to the field of computational biology calculations, in particular to a computational simulation method for protein-protein docking. Background technique [0003] In the post-genomic era, the interaction between biomacromolecules has received more and more attention. Understanding how different biomolecular monomers work together requires knowledge of the structure of the complex. However, the expected number of biomolecular complexes will be at least an order of magnitude higher than the number of protein molecules in the proteome, and they are difficult to study with classical methods such as nuclear magnetic resonance and X-ray crystallography. Therefore, when it is necessary to do structure-based prediction of the three-dimensional structure of the complex, computational methods such as docking are very important. [0004] Molecular docking is one of the important methods of molecular simulation. Its essence is the re...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/10
Inventor 金莲
Owner LANGCHAO ELECTRONIC INFORMATION IND CO LTD
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