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Method for constructing plant protein interaction network

A plant protein, interaction network technology, applied in proteomics, bioinformatics, special data processing applications, etc., can solve problems such as limiting the accuracy of the method

Active Publication Date: 2018-02-02
SHANGHAI JIAOTONG UNIV
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Problems solved by technology

Although these methods utilize different types of biological data resources to predict protein interaction relationships, these methods are all based on indirect evidence of non-structural features, which limits the accuracy of the method

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  • Method for constructing plant protein interaction network
  • Method for constructing plant protein interaction network

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Embodiment Construction

[0016] The following takes the construction of protein interaction network at the whole genome level of rice as an example, refer to figure 1 , to specifically illustrate the specific implementation steps of the method for constructing a plant protein interaction network of the present invention.

[0017] Step 1. Isolate non-transposon-related genes from the rice genome, and construct a stable rice protein structure model with Modeller homology modeling software. The screening criteria meet one of the following conditions: local sequence alignment tool BLAST E value-5 , or MPQS (ModPipe quality score) value ≥ 0.5, or GA341 value ≥ 0.5, or z-DOPE value < 0.

[0018] Step 2. Collect spatial structure data of homologous or heterologous protein complexes from PDB and PISA databases, and use PIBASE software package to calculate the structure of the interaction interface between each chain of the protein complex (interface structures) and the corresponding interaction residues. Use ...

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Abstract

The present invention provides a vegetable protein interaction network construction method. The method comprises: combining a protein structure with a non-structure feature; training a protein interaction model by using a random forest algorithm; predicting a vegetable protein interaction relationship by using a trained protein interaction classifier; and then constructing a vegetable protein interaction relationship network. Compared with the existing method, the method greatly improves accuracy of vegetable protein interaction relationship prediction.

Description

technical field [0001] The invention relates to biotechnology, in particular to a method for constructing a plant protein interaction network. Background technique [0002] The interaction between proteins is essential to almost all cellular processes, and most genes perform biological functions by interacting with other proteins at the protein level. At present, some experimental methods have been developed, such as yeast two-hybrid, affinity purification and other technical methods to analyze the interaction relationship of proteins. With the rapid increase of completed genome sequence information, the understanding of the relationship between genes / proteins has lagged far behind the growth of gene sequences, and the experimental methods for analyzing protein interactions not only have low throughput, but also require high technology , it is difficult to carry out related research work on a large scale. [0003] In the past ten years, many computer-based methods have bee...

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/18
CPCG16B20/00
Inventor 张利达刘诗薇刘奕慧
Owner SHANGHAI JIAOTONG UNIV