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Protein function labeling method and system

A protein function and protein technology, applied in the field of bioinformatics, can solve the problems of high cost and low efficiency of biological experiment methods, and achieve the effect of solving high cost, low efficiency and improving performance

Active Publication Date: 2019-04-30
CENT SOUTH UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0005] The purpose of the present invention is to disclose a protein function labeling method and system to improve the performance of protein labeling and solve the problems of high cost and low efficiency of biological experiment methods

Method used

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  • Protein function labeling method and system
  • Protein function labeling method and system
  • Protein function labeling method and system

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Experimental program
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Embodiment 1

[0031] This embodiment discloses a method for labeling protein functions, such as figure 1 Shown, including:

[0032] Step S1: Find the neighbors of the first-level structure according to the representative structure of the protein to be queried.

[0033] In this step, the function of the protein can be inferred based on the structural similarity of the protein, especially the distant three-dimensional structural similarity. For a given protein Q to be queried, obtain a representative structure M from the PDB library or homology model database, and use the structure neighbor search algorithm to find all the structural neighbors of M in the protein structure library to form the first-level structure neighbors (N1, N2 ,...).

[0034] Step S2: Search for the homologous sequence of the protein to be queried, and find the secondary structure neighbors of the protein to be queried according to the representative structure of the homologous sequence.

[0035] In this step, you can use the s...

Embodiment 2

[0071] Corresponding to the foregoing method embodiment, this embodiment discloses a protein function labeling system, including:

[0072] The first processing module is used to find the neighbors of the first-level structure according to the representative structure of the protein to be queried;

[0073] The second processing module is used to search for the homologous sequence of the protein to be queried, and to find the secondary structure neighbors of the protein to be queried according to the representative structure of the homologous sequence;

[0074] The third processing module is used to evaluate the first possibility that the function appears in the protein to be queried according to the distribution of a certain function of the first-level structure neighbors and the second-level structure neighbors; and according to all The homologous sequence evaluates the second possibility that the function appears in the protein to be queried according to the distribution of the func...

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Abstract

The invention relates to the technical field of bioinformation, and discloses a marking method and system for protein functions. Therefore, protein marking performance is improved, expensive cost of a bioexperiment method and poor efficiency are solved. The method comprises following steps: estimating the first possibility of a certain function in a to-be-inquired protein according to a first-stage structure neighborhood and a second-stage structure neighborhood; estimating the second possibility of the certain function in the to-be-inquired protein according to all homologous sequences; inputting a PSSM matrix of the to-be-inquired protein into an SVM prediction model to obtain the third possibility of the certain function in the to-be-inquired protein; converting the distribution of the function corresponding to other species according to the gene co-expression fraction into the fourth possibility of the function occurring in a target species in the to-be-inquired protein; and mixing the first possibility, the second possibility, the third possibility and the fourth possibility to estimate the comprehensive possibility of the function in the to-be-inquired protein.

Description

Technical field [0001] The present invention relates to the field of biological information technology, in particular to a protein function labeling method and system. Background technique [0002] Protein is the material basis of all life and the ultimate controller and direct executor of life activities. It participates in almost all life activities in the organism, such as heredity, development, reproduction, material and energy metabolism, stress, thinking and memory Wait. The protein is composed of 20 different amino acid residues connected to each other by peptide bonds. After being folded into a specific spatial conformation, the protein has the corresponding biological activity and function. From the physiological point of view, protein function includes: enzyme catalysis, material transport and storage, nutrient storage, movement coordination, mechanical support, immune protection, signal reception and conduction, growth and differentiation control, etc. Human beings p...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/00
CPCG16B20/00
Inventor 邓磊曾丞
Owner CENT SOUTH UNIV
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