Method for calculating and identifying protein-RNA interaction sites

A technology of interaction site and recognition method, which is applied in the field of biomacromolecule interaction recognition, can solve the problems of low prediction accuracy and inability to obtain high sensitivity and specificity at the same time, achieve good generalization performance and ensure prediction Ability, the effect of preventing overfitting

Inactive Publication Date: 2010-05-19
CHONGQING UNIV
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Problems solved by technology

[0003] However, the existing identification methods all have the problem of not being able to obtain high sensitivity and specificity at the same time, and the prediction accuracy is still not high (Terribilini

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  • Method for calculating and identifying protein-RNA interaction sites

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Embodiment Construction

[0012] The following is a detailed description of the use of the method of the present invention for protein-RNA interaction site identification as an example, including the following steps:

[0013] a) Select 640 kinds of two-dimensional property parameters of 20 kinds of natural amino acids, including: molecular electrical interaction vector, molecular electric distance vector and holographic molecular electric distance vector, topology, topological charge index, number of rotations and paths, edge adjacency index, Burden eigenvalue, autocorrelation, connectivity index, information index and eigenvalue index.

[0014] Table 1 12 principal component scores of 640 two-dimensional property parameters of 20 natural amino acids

[0015]

[0016] a The 20 natural amino acids are represented by conventional single English letters.

[0017] Using principal component analysis to process 640 kinds of property parameters, 12 principal components are obtained, which accumulatively ...

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Abstract

The invention discloses a method for calculating and identifying protein-RNA interaction sites, which comprises the following steps: a) establishing a protein structure characterization method-amino acid two-dimensional character scoring based on the active ingredient analysis method; b) using the amino acid two-dimensional character scoring for characterizing the structure features of the protein-RNA interaction sites; c) using the genetic algorithm for selecting feature parameters which are closely related to the protein-RNA interaction sites; and d) establishing a protein-RNA interaction site identification model by applying a radial basis kernel support vector machine, and respectively using three methods of self-replacement verification, retaining 1/5 cross-verification and external verification for verifying the predictive capability of the model. The method can be used for prediction and specificity analysis of the protein-RNA interaction sites and is vital for deep understanding of gene expression regulation, protein synthesis and replication, assembly and other processes of a variety of virus.

Description

technical field [0001] The invention relates to a biomacromolecule interaction identification method, in particular to a method for calculating and identifying interaction sites between proteins and RNAs. Background technique [0002] Protein-RNA interaction plays an important role in many biological activities, involving the regulation of gene expression, protein synthesis, and the replication and assembly of many viruses (Noller, Science, 2005, 309: 1508). Computational identification of protein-RNA interaction is crucial for designing biological experiments and analyzing the characteristics of the interaction between the two, and for in-depth understanding of how proteins recognize RNA. However, the prediction of protein-RNA interaction sites has only started in recent years. The main reason is the low number of protein and RNA complex structures that have been measured. Currently developed methods include neural network (Jeong et al., Genome Inform.Ser.Workshop Genome ...

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Application Information

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IPC IPC(8): G06F19/00
Inventor 梁桂兆马秀岩赵巍杨力梅虎
Owner CHONGQING UNIV
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