A Spatial Optimization Method for Protein Conformation Based on Local Structure Alignment
A technology of local structure and optimization method, applied in the direction of proteomics, analysis of two-dimensional or three-dimensional molecular structure, genomics, etc., can solve the problems of low sampling efficiency and low prediction accuracy, so as to improve the prediction accuracy and search The effect of efficiency
Active Publication Date: 2021-04-06
ZHEJIANG UNIV OF TECH
View PDF6 Cites 0 Cited by
- Summary
- Abstract
- Description
- Claims
- Application Information
AI Technical Summary
Problems solved by technology
[0006] In order to overcome the shortcomings of low sampling efficiency and low prediction accuracy in the existing protein conformation space optimization methods, the present invention proposes a protein conformation space optimization method based on local structure alignment with high sampling efficiency and high prediction accuracy
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 moreImage
Smart Image Click on the blue labels to locate them in the text.
Smart ImageViewing Examples
Examples
Experimental program
Comparison scheme
Effect test
Embodiment Construction
[0041] The present invention will be further described below in conjunction with the accompanying drawings.
[0042] refer to Figure 1 ~ Figure 3 , a method for optimizing protein conformation space based on local structure alignment, the method comprising the following steps:
[0043] 1) given input sequence information;
[0044] 2) Select the Rosetta score3 energy function E(x), and obtain the fragment library according to ROBETTA;
[0045] 3) Parameter initialization: set the population size Ps, the iteration counter g, the maximum genetic algebra G max , initial population search track length N, temperature factor KT, segment length m, parameter n;
[0046] 4) Initialize the population: start Ps Monte Carlo trajectories, search N times for each trajectory, and generate Ps initial individuals;
[0047] 5) For each target individual x i ,i∈{i=1,2,...,Ps} performs the following operations:
[0048] 5.1) Randomly select an individual x j ,j∈{1,2,...,Ps} and j≠i, perform ...
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
Login to View More Abstract
A protein conformation space optimization method based on local structure alignment. Under the basic framework of evolutionary algorithm, a search strategy based on local structure alignment is used to randomly select a fragment to insert into the window, and the original The fragment information of the fragment library is compared with the fragment information in the fragment library, and a potential fragment is selected for structural replacement according to the two structure comparison indicators; finally, the population update is guided by the Monte Carlo mechanism, and the potential conformation is selected to enter the next step. generation population. The invention proposes a protein conformation space optimization method based on local structure alignment with high prediction accuracy and low calculation cost.
Description
technical field [0001] The invention relates to the fields of biological informatics, intelligent optimization and computer application, and in particular to a protein conformation space optimization method based on local structure comparison. Background technique [0002] Proteins are the main bearers of life activities, and the diversity of their structures determines the diversity of their functions. Precisely predicting the spatial structure of proteins is of great significance to biopharmaceuticals and disease research. The use of biochemical methods to determine protein structures is costly and time-consuming. Therefore, the use of computational methods to predict the three-dimensional structure of proteins has gradually become an important topic in computational biology. [0003] In recent years, de novo prediction methods have achieved good results in the field of protein structure prediction. However, as far as the current technical means are concerned, the ab init...
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
Login to View More Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/20G16B15/20
Inventor 张贵军王小奇谢腾宇周晓根马来发郝小虎
Owner ZHEJIANG UNIV OF TECH