Template-based multi-domain protein structure assembling method

An assembly method and domain protein technology, which can be used in the analysis of two-dimensional or three-dimensional molecular structures, special data processing applications, instruments, etc., can solve problems such as low prediction accuracy, inability to determine the direction of domain protein assembly, and lack of template guidance. To achieve the effect of improving the forecast progress

Active Publication Date: 2017-09-19
ZHEJIANG UNIV OF TECH
View PDF4 Cites 6 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, due to the lack of template guidance in the above method, the assembly direction of the domain protein cannot be determined during assembly, resulting

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Template-based multi-domain protein structure assembling method
  • Template-based multi-domain protein structure assembling method
  • Template-based multi-domain protein structure assembling method

Examples

Experimental program
Comparison scheme
Effect test

Embodiment Construction

[0046]The present invention will be further described below in conjunction with the accompanying drawings.

[0047] refer to figure 1 and figure 2 , a method for assembling a template-based multi-domain protein structure, comprising the following steps:

[0048] 1) Input the three-dimensional structure of each single-domain protein and the sequence information of its corresponding multi-domain protein;

[0049] 2) Set the maximum number of iterations I max , conflict distance threshold d clash , the interaction threshold d contact , the interacting atomic number constant n 0 ;

[0050] 3) Perform the following operations for each multi-domain protein in the PDB (Protein Data Bank) library to determine the assembly template:

[0051] 3.1) Find the best alignment position of the first protein according to the protein structure alignment tool TM-align, and record its template alignment score TM-score 1 ;

[0052] 3.2) Starting from the last residue position of the first...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

PUM

No PUM Login to view more

Abstract

The invention discloses a template-based multi-domain protein structure assembling method. The method comprises the steps of firstly, comparing domain proteins once by utilizing a protein structure comparison tool TM-align according to the structures of the domain proteins, and finding out an optimal template from a multi-domain protein database; secondly, obtaining a rotation and translation matrix by utilizing a Kabsch method, overlapping the domain proteins to the template, and performing translation and rotation operations on the domain proteins, thereby enabling a distance between the domain proteins to be equal to a minimum allowed distance; thirdly, performing adjustment by performing random translation and rotation on an assembled structure, and measuring the quality of the assembled structure by utilizing a conflict factor between the domain proteins, an interactive atom quantity and a moving range of the assembled structure relative to the template; and in an assembling process, assembling the adjacent domain proteins in sequence, fixing the assembled structures, and when all the structures are assembled, outputting a final assembling result. The template-based multi-domain protein structure assembling method provided by the invention is relatively high in prediction precision.

Description

technical field [0001] The invention relates to the fields of biological informatics, intelligent optimization and computer application, and in particular to a template-based multi-domain protein structure assembly method. Background technique [0002] Large-scale proteins are usually composed of multiple independently folded domain proteins, and the determination of the structure of multi-domain proteins can greatly promote the progress of biological research. Domain proteins usually have a compact three-dimensional structure and specific biological functions, and the same domain protein may have different structures. In addition, the single-domain three-dimensional structure of many multi-domain proteins has been determined by X-ray diffraction, nuclear magnetic resonance and computer prediction. Therefore, it is an important step to obtain the structure of the corresponding multi-domain protein based on the structure of the single-domain protein, and a necessary link to ...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to view more

Application Information

Patent Timeline
no application Login to view more
IPC IPC(8): G06F19/16
CPCG16B15/00
Inventor 张贵军周晓根郝小虎王柳静
Owner ZHEJIANG UNIV OF TECH
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Try Eureka
PatSnap group products

Browse by: Latest US Patents, China's latest patents, Technical Efficacy Thesaurus, Application Domain, Technology Topic.

© 2024 PatSnap. All rights reserved.Legal|Privacy policy|Modern Slavery Act Transparency Statement|Sitemap