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Method for extracting protein-micromolecule interaction module

A technology for small molecules and proteins, applied in the field of protein research, it can solve the problems of general alignment effect and inability to find protein-small molecule interaction modules.

Active Publication Date: 2016-02-24
UNIV OF SCI & TECH OF CHINA
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, due to the flexibility of small molecules, the three-dimensional structure alignment effect using small molecules as a reference is usually mediocre in practice, and the interaction modules of protein-small molecule binding cannot be found well.
Thus, quite a few studies actually discover protein-small molecule interaction modules empirically through manual inspection by biologists

Method used

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  • Method for extracting protein-micromolecule interaction module
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  • Method for extracting protein-micromolecule interaction module

Examples

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Effect test

Embodiment 1

[0063] Example 1: Extraction of interaction modules bound to small molecule ATP and analysis of their biological significance.

[0064] 1.1 Background introduction

[0065] Adenosine triphosphate (referred to as ATP) is an unstable high-energy compound consisting of 1 molecule of adenine, 1 molecule of ribose and 3 molecules of phosphoric acid. Also known as adenosine triphosphate, referred to as ATP. Because ATP can release a large amount of energy when it is hydrolyzed, it is the most direct energy source in the organism. ATP participates in most metabolic processes in the organism and is one of the most important small molecules. Many related studies have shown that proteins of different protein families have conserved binding modules in the ATP-binding pocket. Extracting and analyzing these conserved modules will provide important guidance for understanding the ATP binding mechanism and drug design for ATP-related metabolic diseases significance.

[0066] 1.2 Data proce...

Embodiment 2

[0071] Example 2: Extraction of interaction modules combined with small molecule DIG and its application in protein design.

[0072] 2.1 Background introduction

[0073] With the rapid development of protein science, the scientific community has a deeper understanding of proteins, and protein design has become an important topic in biology, especially in synthetic biology. One of the most authoritative research teams in this field, David Baker's laboratory at the University of Washington, published a landmark work in the top international academic journal Nature in 2013, that is, the DIG (Chinese name Digaoxin) was obtained through artificial design. , a drug small molecule for the treatment of heart disease) is an artificial protein with high binding activity, showing the unlimited potential of artificially designing various small molecule binding proteins (C.E. :10.1038 / nature12443). In the process of protein design, how to determine the binding pocket or active center of ...

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Abstract

The invention relates to a method for extracting a protein-micromolecule interaction module. The method specifically comprises: firstly, performing quantitative description on atoms (or amino acids) forming a micromolecular binding pocket on protein according to properties of the atoms (or amino acids); secondly, estimating the distance between the every two pocket atoms (or amino acids), and establishing a distance matrix; thirdly, extracting categories of the pocket atoms (or amino acids) with similar properties by utilizing a clustering algorithm; and finally, performing post-processing to obtain the protein-micromolecule interaction module. The method can be applied to multiple aspects of bioinformatics research, protein design, drug screening, micromolecular chemical synthesis and the like.

Description

technical field [0001] The invention belongs to the technical field of protein research, and specifically relates to the extraction of interaction modules combining proteins and small molecules using structural biology data, which can be applied to multiple aspects such as bioinformatics research, protein design, drug screening, and small molecule chemical synthesis. technical background [0002] Based on the basic biological assumption that the three-dimensional structure of a protein determines its function, protein pockets that can bind the same or similar small molecules also have the same or similar three-dimensional functional modules in theory. Extracting these functional modules can provide important structural biology clues for protein engineering, drug screening and protein design. Traditional computer-based protein-small molecule interaction module discovery methods usually use the small molecule as a reference to perform three-dimensional structural alignment of ...

Claims

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Application Information

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IPC IPC(8): G06F19/18
Inventor 梁治牛立文滕脉坤何巍
Owner UNIV OF SCI & TECH OF CHINA
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