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Method for predicting protein bound with ribonucleic acid

A prediction method and ribonucleic acid technology, applied in proteomics, genomics, instruments, etc., can solve the problem of low accuracy of RBP, and achieve the effect of reducing the amount of calculation, accurate prediction model, and comprehensive and accurate prediction

Active Publication Date: 2017-03-22
HUAZHONG UNIV OF SCI & TECH
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0004] Aiming at the above defects or improvement needs of the prior art, the present invention provides a method for predicting proteins combined with ribonucleic acid, the purpose of which is to select an appropriate feature vector, thereby solving the problem of the low accuracy of the prior art for the prediction of RBP technical issues

Method used

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  • Method for predicting protein bound with ribonucleic acid
  • Method for predicting protein bound with ribonucleic acid
  • Method for predicting protein bound with ribonucleic acid

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0118] The prediction method of embodiment 1 includes the selection of feature vectors, the construction of prediction models and the prediction of the target protein to be predicted;

[0119] S1. figure 2 It is a flow chart of selecting eigenvectors in Embodiment 1 of the invention, including the first eigenvector to the eighth eigenvector; respectively corresponding to the hydrophobicity of the amino acids contained in the protein, the polarity of the amino acids contained in the protein, and the normalized range of the amino acids contained in the protein De Waals volume, the polarizability of amino acids contained in proteins, the secondary structure of proteins, the solvent accessibility of proteins; the charge and polarity of the side chains of amino acids contained in proteins; and the evolution information of proteins;

[0120] S11. Wherein, the first eigenvector to the sixth eigenvector are obtained by using the encoding method of the global protein sequence descript...

Embodiment 2

[0187] According to the above steps of S4, the human protein dataset was tested as the target protein, and the human protein dataset included 967 RBPs and 579 non-redundant non-RBPs. The prediction results are as follows: 84% of 967 RBPs are correctly predicted, 97% of 597 non-RBPs are correctly predicted, and the Matthew correlation coefficient is 0.788.

Embodiment 3

[0189] Repeat Example 2 with the same steps described above, the difference is that the target protein is the protein data set of yeast, and the corresponding Matthew correlation coefficient is 0.729.

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Abstract

The invention discloses a method for predicting a protein (RBP) bound with ribonucleic acid. The method comprises the steps of firstly, obtaining a total candidate feature set of a sample protein according to characteristics of amino acid; secondly, selecting W optimal features from the total candidate feature set to serve as eigenvectors; thirdly, building a prediction model according to the eigenvectors and protein characteristics of the sample protein; and finally, obtaining a prediction result of protein characteristics of a to-be-predicted protein according to eigenvectors of the to-be-predicted protein. According to the method, the total candidate feature set covers various characteristics of amino acid; various factors influencing the performance of binding the protein to ribonucleic acid are comprehensively considered; and the accuracy exceeds 90% through verification, the accuracy in the prior art is improved by 35%, a Mathew correlation coefficient is 0.788, and the Mathew correlation coefficient in the prior art is increased by two times, so that the prediction is more comprehensive and accurate.

Description

technical field [0001] The invention belongs to the field of prediction of interaction between biomacromolecules, and more specifically relates to a prediction method of protein (RBP) combined with ribonucleic acid. Background technique [0002] Proteins that can bind to ribonucleic acid (RNA) are called ribonucleic acid binding proteins (RBP), and proteins that cannot bind to ribonucleic acid are called non-ribonucleic acid binding proteins (non-RBP). In organisms, RBP interacts with ribonucleic acid (RNA) to form a complex, which plays an important role in many biological processes, such as post-transcriptional gene regulation, variable splicing and translation of genes, etc., so it is predicted whether the protein is RBP Very important. [0003] Non-patent literature (Zhao, H., Y.Yang, and Y.Zhou,. RNA biology, 2011.8 (6): p.988-996) discloses a high-precision ribonucleic acid binding protein prediction method (SPOT- seq). This method constructs a template library base...

Claims

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Application Information

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IPC IPC(8): G06F19/18
CPCG16B20/00
Inventor 刘士勇张晓利
Owner HUAZHONG UNIV OF SCI & TECH
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