Method for calculating and simulating protein-protein docking

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...

AI Technical Summary

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.

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