Method for identifying protein functions based on protein-protein interaction network and network topological structure features

Abstract

The invention discloses a method for identifying protein functions based on a protein-protein interaction network and network topological structure features. Firstly, a node and side-weighted protein-protection interaction network is established, wherein the node represents protein while the edge represents the interaction; then the nodes and the sides in the network are weighted by protein first-grade structural description and protein-protein interaction trust scoring; protection functional annotation data is collected to establish a data set, and a new protein with overall and local information network topological structure features is provided based on a graph theory; and finally, the protein functions are predicated by choosing features through adopting a minimum-redundancy maximum-correlation method and by modeling through a support vector machine. The protein function predication method is greatly better than the prior art, and has robustness on sequence similarity and sampling; and meanwhile, information of three-dimensional structure and the like of protein is not required, so that the method is simple, rapid, accurate and efficient, and the method is expected to be applied in the research fields of proteomics and the like.

Description

technical field [0001] The invention belongs to the technical field of proteomics technology. More specifically, it relates to a method for identifying protein functions based on protein interaction networks and network topology features. Background technique [0002] A protein is a biomacromolecule composed of one or more peptide chains, and is the basic functional unit of cells. In organisms, proteins perform a variety of biological functions, such as DNA replication and transcription, catalyzing biological reactions, transporting biologically active molecules, etc. Therefore, the functional annotation of proteins is an important step in elucidating the nature of life at the molecular level, and plays an important role in the study of pathological mechanisms and the identification of potential drug targets. With the rapid development of high-throughput sequencing technology, various databases have stored massive amounts of protein sequence information. However, only a s...

AI Technical Summary

Problems solved by technology

However, these methods have some defects, for example: homology-based methods do not take into account the fact that homologous proteins can acquire different biological functions in the long evolutionary process

Structural similarity-based methods do not take into account the fact that even though the three-dimensional structures of two proteins are highly similar, changes in key active site residues can alter the biological function of the protein

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