Identification of key flexible amino acids in the binding pocket of small protein molecules

Abstract

The present invention relates to a method for identifying key flexible amino acids on protein small molecule binding pockets, comprising the following steps: Step 1, in the protein PDB structure, the structure of the protein is classified into different subtype clusters by 95% sequence similarity; Step 2, clear biological ligands, overlap all protein structures in the same structural subtype cluster, and accurately identify small molecule binding pockets on the protein; Binding sites, divided into site-binding subtypes according to the small molecule binding position; step 4, study the nature of protein flexibility by calculating the difference characterization factors of physicochemical and structural parameters; step 5, use the highest score of the system that forms the protein binding pocket to Identify key flexible residues. A unified and unbiased research process system was designed, and a systematic mathematical and statistical formula was developed to determine the structural flexibility of the binding site amino acids at the same position in different structural models.

Description

technical field [0001] The invention relates to the field of computational biotechnology, in particular to a method for identifying key flexible amino acids on protein small molecule binding pockets. Background technique [0002] Protein is the material basis of life, and the three-dimensional structure of protein is the basic condition for reflecting its own biochemical function and cell function. During the process of performing biological functions, proteins constantly change their conformation and produce physical, chemical and biological reactions with the surrounding environment. This structural flexibility feature is closely related to the physiological properties of the protein's own structural and functional domains, molecular recognition and binding mechanisms, and catalytic activity, and plays an extremely important role in the normal physiological functions and biological performance of proteins. [0003] At present, the virtual drug screening technology based o...

AI Technical Summary

Problems solved by technology

However, there are not many studies that systematically explore the conformational flexibility characteristics of proteins as a whole or local regions, determine the binding sites at the amino acid level, and predict the properties of key flexible residues at the atomic level.

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