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Protein conformational space optimization method based on fragment assembly

An optimization method, protein technology, applied in the field of bioinformatics, computer application

Active Publication Date: 2014-12-10
ZHEJIANG UNIV OF TECH
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0003] The biggest challenge facing the protein conformation optimization problem is to search the extremely complex protein energy function surface

Method used

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  • Protein conformational space optimization method based on fragment assembly
  • Protein conformational space optimization method based on fragment assembly
  • Protein conformational space optimization method based on fragment assembly

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Embodiment Construction

[0033] The present invention will be further described below in conjunction with the accompanying drawings.

[0034] refer to figure 1 , a dynamic step size search method in conformation space, comprising the following steps:

[0035] 1) Initialize the population: Randomly select fragments from the protein fragment library to generate a population P of popSize individuals int , and set the algorithm parameters: population size popSize, protein sequence length Length (that is, the dimension of the optimization problem), the number of iterations T of the algorithm, the crossover factor CR of the algorithm, and the length L of the protein fragment.

[0036] 2) Calculate the function value of each population according to the scoring function f, and sort them, where P max The function value of is optimal.

[0037] 3) When the set termination condition is not reached, perform the following operations

[0038] 3.1) For population P int Each individual P in i Do the following: ...

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Abstract

The invention discloses a protein conformational space optimization method based on fragment assembly. The protein conformational space optimization method includes the following steps that fragments are selected from a protein fragment library randomly to generate population individuals, the function value of each population can be calculated according to a scoring function, sorting is conducted, the optimal function value is obtained, crossover and variation operation is carried out on the individuals in each population, so that the populations are updated, and iterative operation is performed until a set terminal condition is met. The effective conformational space optimization method is provided.

Description

technical field [0001] The invention relates to the fields of bioinformatics and computer applications, in particular to a method for optimizing protein conformation space based on fragment assembly. Background technique [0002] The successful drawing of the human genome sequence map means that all the predetermined goals of the Human Genome Project have been realized, and it also marks the successful completion of the Human Genome Project and the advent of the post-genome era. In the post-genome era, the focus of research has shifted from gene sequencing to the identification of genome functions: predicting the spatial structure of protein molecules based on their amino acid sequences. This will enable people to more systematically understand the genetic information transmission process of biological information from DNA to biologically active proteins, so that the central dogma can be clarified in more detail, and then have a further deep understanding of various phenomen...

Claims

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Application Information

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IPC IPC(8): G06F19/16
Inventor 张贵军郝小虎周晓根秦传庆梅珊
Owner ZHEJIANG UNIV OF TECH
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