A method for assembling discontinuous multi-domain protein structures
An assembly method and domain protein technology, which is applied in the field of structural assembly of discontinuous multi-domain proteins, can solve the problem of low prediction accuracy and achieve the effect of improving prediction accuracy and search efficiency
Active Publication Date: 2020-12-01
ZHEJIANG UNIV OF TECH
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[0005] In order to overcome the disadvantages of low prediction accuracy of existing discontinuous multi-domain protein structure assembly methods, the present invention provides a discontinuous multi-domain protein structure assembly method with high prediction accuracy
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[0042] The present invention will be further described below in conjunction with the accompanying drawings.
[0043] refer to figure 1 with figure 2 , a discontinuous multi-domain protein structure assembly method, comprising the following steps:
[0044] 1) Input the sequence information of the protein to be assembled and the three-dimensional structure of each single domain;
[0045] 2) Set the maximum number of iterations G max , the number of assembly templates T, the conflict distance threshold d clash and the interaction threshold dcontact ;
[0046] 3) Use the protein sequence alignment tool FFAS3D to search for the top T template proteins with the highest scores from the protein library;
[0047] 4) Perform the following operations for each template protein:
[0048] 4.1) Overlap each single domain of the protein to be assembled on the template according to the FFAS3D sequence alignment information;
[0049] 4.2) Fix the discontinuous single-domain protein, and...
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The invention discloses a discontinuous multi-domain protein structure assembly method. The method comprises the steps of firstly, quickly searching for a protein library by utilizing a protein sequence threading comparison tool, and selecting out multiple templates with the highest scores; secondly, according to threading comparison information, accurately overlapping single-domain structures tothe templates, thereby extracting direction information in the templates; thirdly, performing random rotation and translation operations on a structure obtained by overlapping, measuring the quality of the current structure by interaction and a conflict distance between domains, adding a template control factor for preventing an assembled structure from deviating from the directions of the templates, and adding a boundary distance factor for facilitating boundaries of continuous and discontinuous domain proteins to be fully connected; and finally, according to energy, selecting out an optimalstructure obtained by multiple template groups. The discontinuous multi-domain protein structure assembly 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, in particular to a structure assembly method of a discontinuous multi-domain protein. Background technique [0002] More than 70% of the proteins in the protein library are multi-domain proteins, that is, a protein contains multiple substructures. Among these multi-domain proteins, more than 40% of the proteins contain one or more discrete single-domain proteins, for example, in the CATH protein database, more than 15% of the proteins are multi-domain proteins, of which more than 18% of the proteins contain at least A discontinuous domain protein. For these single-domain proteins, their corresponding sequences are discontinuous and divided into multiple parts, but for three-dimensional structures, although they are divided into multiple parts, they all belong to one domain. It can be seen that discontinuous multi-domain proteins account f...
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IPC IPC(8): G16B15/20
CPCG16B15/00
Inventor 张贵军周晓根郝小虎王柳静
Owner ZHEJIANG UNIV OF TECH