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A method for assembling multidomain protein structures based on interdomain residue contacts

An assembly method and domain protein technology, which can be used in bioinformatics, hybridization, instrumentation, etc., can solve problems such as low accuracy, and achieve the effect of improving prediction accuracy

Active Publication Date: 2021-02-26
ZHEJIANG UNIV OF TECH
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Problems solved by technology

[0006] In order to overcome the low precision of existing multi-domain protein assembly methods, the present invention proposes a multi-domain protein structure assembly method based on inter-domain residue contacts with higher precision

Method used

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  • A method for assembling multidomain protein structures based on interdomain residue contacts
  • A method for assembling multidomain protein structures based on interdomain residue contacts
  • A method for assembling multidomain protein structures based on interdomain residue contacts

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Embodiment Construction

[0042] The present invention will be further described below in conjunction with the accompanying drawings.

[0043] refer to figure 1 and figure 2, a multi-domain protein structure assembly method based on interdomain residue contacts, comprising the following steps:

[0044] 1) Given the three-dimensional structure and full-length sequence information of each domain of the protein to be assembled;

[0045] 2) Parameter setting: set the maximum number of iterations I max , conflict distance threshold d clash , the number of assembled templates T, the temperature length K, the contact energy depth d well ;

[0046] 3) Use the structural alignment tool TM-align (https: / / zhanglab.ccmb.med.umich.edu / TM-align / ) to each of the protein PDB library (http: / / www.rcsb.org / ) Multi-domain protein is scored, and the score of each template is the average value of TM-score (https: / / zhanglab.ccmb.med.umich.edu / TM-score / ) between each domain and the template, and the score is selected ...

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Abstract

A multi-domain protein structure assembly method based on residue contacts between domains, starting from the three-dimensional structure of each domain, using a structure comparison tool to score all multi-domain protein templates in the protein library, and select the template with the highest score for Assembly; an initial structure is then generated from the template, and a small region is randomly selected for rigid-body rotation and translation, resulting in a new full-length structure; secondly, the assembly is evaluated in terms of inter-domain residue contacts, template and inter-domain atomic conflict energies The quality of the structure, and accept the assembled structure according to the Monte Carlo criterion; finally, the structure with the lowest energy among the structures assembled by all templates is selected as the final structure. The invention provides a multi-domain protein structure assembly method based on inter-domain residue contacts with high prediction accuracy.

Description

technical field [0001] The invention relates to the fields of intelligent optimization, biological information and computer application, in particular to a multi-domain protein structure assembly method based on residue contact between domains. Background technique [0002] Large-scale proteins often consist of multiple independently folded domain proteins. Although each domain protein can complete biological functions independently, multiple domains combined can complete biological functions that independent domain proteins cannot complete. In addition, many biological functions depend on the interaction between domains, for example, many enzymes realize their functions between the contact surfaces of different domains. Statistics show that in nature, at least 90% of eukaryotic proteins and 67% of prokaryotic proteins contain multiple domains. [0003] In current protein libraries, most multi-domain proteins are treated as single-domain proteins. Currently, there are mor...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B25/10G16B35/20
CPCG16B25/10G16B35/20
Inventor 周晓根张贵军彭春祥胡俊
Owner ZHEJIANG UNIV OF TECH
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