Marking method and system for protein functions

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

Active Publication Date: 2017-04-26
CENT SOUTH UNIV
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  • 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

Method used

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  • Marking method and system for protein functions
  • Marking method and system for protein functions
  • Marking method and system for protein functions

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Embodiment 1

[0031] This embodiment discloses a protein function labeling method, such as figure 1 shown, including:

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

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

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

[0035] In this step, all homologous sequenc...

Embodiment 2

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

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

[0073] The second processing module is used to search the homologous sequence of the protein to be queried, and find the neighbors of the secondary structure 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 of the function appearing in the protein to be queried according to the distribution of a certain function of the first-order structure neighbors and the second-order structure neighbors; and based on all the The distribution of homologous sequences against the function evaluates the second possibility that the function occurs in the protein to be queried;

[00...

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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 invention relates to the technical field of biological information, in particular to a protein function labeling method and system. Background technique [0002] Protein is the material basis of all life, the ultimate controller and direct executor of life activities, and it participates in almost all life activities in organisms, such as heredity, development, reproduction, metabolism of matter and energy, stress, thinking and memory Wait. Proteins are composed of 20 different amino acid residues connected to each other through peptide bonds. After being folded into a specific spatial conformation, the protein has corresponding biological activities and functions. From a physiological point of view, protein function includes: enzyme catalysis, material transport and storage, nutrient storage, motor coordination, mechanical support, immune protection, signal acceptance and transduction, growth and differentiation control, etc. Humans pay attentio...

Claims

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Application Information

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IPC IPC(8): G06F19/18
CPCG16B20/00
Inventor 邓磊曾丞
Owner CENT SOUTH UNIV
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