Predicting method of nucleic acid binding site bound with protein or micromolecule

A prediction method and binding site technology, applied in proteomics, instrumentation, genomics, etc., can solve the problems of low prediction success rate and multiple false positive results, and achieve the goal of simple method, convenient use, and improved prediction success rate. Effect

Inactive Publication Date: 2019-07-05
HUAZHONG NORMAL UNIV
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  • Application Information

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Problems solved by technology

[0004] Existing methods for predicting nucleic acid binding sites judge potential nucleotide binding sites by calculating the distance information bet

Method used

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  • Predicting method of nucleic acid binding site bound with protein or micromolecule
  • Predicting method of nucleic acid binding site bound with protein or micromolecule
  • Predicting method of nucleic acid binding site bound with protein or micromolecule

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0049] Example 1 nucleic acid-small molecule binding site test set

[0050] There are 22 nucleic acid-small molecule complex structures with a length of 20-94 nucleotides in the test set. The information is shown in Table 1.

[0051] Table 1. Test set information of nucleic acid-small molecule complex experimental structure and the positive predictive value of the method of the present invention

[0052]

[0053]

[0054]

[0055] (1) Nucleic acid structure selection

[0056] Download the experimental tertiary structure of nucleic acid-small molecule complexes in the RCSB PDB database as the initial structure information. Take 1EHT as an example, the nucleic acid is the A chain in the 1EHT.pdb file, with 33 bases, the small molecule is TEP, and its molecular formula is C 7 H 8 N 4 O 2 . Then use RNAComposer structure prediction method to predict the model structure of this nucleic acid. In the same way, the experimental tertiary structure and model structure of the remaining 21 nucl...

Embodiment 2

[0075] Example 2 nucleic acid-protein binding site test set

[0076] The test set consists of 72 nucleic acid-protein complex structures, and the length of the nucleic acid ranges from 20 to 157 nucleotides. The information is shown in Table 4. Replace 22 nucleic acid-small molecule complex structures with 72 nucleic acid-protein complex structures, and repeat all the steps in Example 1. The results show that when using the experimental three-level structure, the prediction success rate of the method of the present invention is 63% (Table 4, attached) figure 1 ). When using the model structure (with 25 nucleic acid-protein complex structures removed, and 47 nucleic acid-protein complex structures remaining), the results show that the average positive predictive value of the method of the present invention, Rsite and Rsite2 methods are 66%, 58% and 56% (Table 5), indicating that the nucleic acid binding site prediction accuracy of the present invention is higher than that of mai...

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Abstract

The invention discloses a predicting method of a nucleic acid binding site bound with a protein or a micromolecule, wherein the method belongs to the field of biomolecule interaction predicting researching and development. The method according to the invention comprises the following steps of using the nucleic acid in a nucleic acid molecule structure as a node in a network model, wherein a shortest distance between two non-continuous nucleic acid heavy atoms in a nucleic acid molecule sequence is smaller than the side of the network model, converting the nucleic acid molecule structure to a nucleic acid molecule network model, determining importance of nucleotide in the nucleic acid molecule through calculating centrality of the node of the nucleic acid network, and if the closeness centrality and the degree centrality of a certain node are higher than summation of average values and standard deviations of all nodes in the whole network, determining the nucleotide which corresponds with the node is the nucleic acid binding site. The predicting method has advantages of realizing high predicting success rate which is higher than that of an existing method, realizing simple operationand high practicability, and realizing an important function in understanding a biological mechanism problem of the nucleic acid and related medicament designing.

Description

Technical field [0001] The invention belongs to the field of biomolecular interaction prediction research and development, and specifically relates to a method for predicting nucleic acid binding sites bound to proteins or small molecules. Background technique [0002] Nucleic acid molecule is one of the basic biological molecules in the living body, and it participates in various life activities in the living body. For example, the aptamer part of the riboswitch can bind to small molecules, and this binding will cause structural changes in the riboswitch, thereby regulating the biological function of the coding part. The discovery of 1,445 nucleic acid viruses has further enriched our understanding of nucleic acid diversity. The rapidly amplified nucleic acid sequence and structure data indicate that nucleic acid is closely related to many diseases such as tumors, nervous system, and cardiovascular diseases. Therefore, understanding the structure and functional mechanism of nu...

Claims

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Application Information

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IPC IPC(8): G16B20/30
Inventor 赵蕴杰王慧雯贾亚曾辰
Owner HUAZHONG NORMAL UNIV
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