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Method and device for predicting three-dimensional protein structure

A prediction method and a technology of three-dimensional structure, applied in special data processing applications, instruments, electrical digital data processing, etc., can solve the problem of low accuracy, achieve the effect of improving accuracy, good prediction effect, and reducing preference

Active Publication Date: 2014-08-27
SUZHOU UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

The prior art discloses the use of genetic algorithms, simulated annealing algorithms and other algorithms to predict the three-dimensional structure of proteins, but the accuracy of prediction using these algorithms is low

Method used

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  • Method and device for predicting three-dimensional protein structure
  • Method and device for predicting three-dimensional protein structure
  • Method and device for predicting three-dimensional protein structure

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0059] see figure 1 , figure 1 It is a flow chart of the method for predicting the three-dimensional structure of a protein provided in Example 1 of the present invention.

[0060] Step S101, select the target ant colony, and initialize the parameters of the ant colony algorithm.

[0061] Step S101 is executed to select the target ant colony, that is, to determine the number of the target ant colony. In this embodiment, the number of ant colonies is determined to be 1, that is, the prediction based on the single ant colony algorithm is performed.

[0062] Initialize the ant colony algorithm parameters, the ant colony algorithm parameters include:

[0063] probability parameter q 1 ; In the present invention, the probability parameter q 1 The value range of is [0, 1], which is set to 0.8 in this embodiment;

[0064] Pheromone τ, its initial value is set to 10 in this embodiment;

[0065] The pheromone volatilization coefficient ρ, in the present invention, the value range...

Embodiment 2

[0149] On the basis of the disclosure of the first embodiment, the present invention also discloses an embodiment, see Figure 4 , Figure 4 It is a flowchart of the method for predicting the three-dimensional structure of a protein provided in Example 2 of the present invention.

[0150] Different from the first example, in the second example, when selecting the target ant colony, p ant colonies are selected, and p>1, that is, in the second example, multiple ant colonies are used to predict the protein structure in parallel. When selecting the target ant colony, the number of the target ant colony can be determined according to the number of processors. In this embodiment, the number of ant colonies is determined to be 8.

[0151] When initializing the parameters of each ant colony algorithm, the 8 target ant colonies share the same pheromone matrix, that is, the 8 target ant colonies share the same pheromone matrix to predict the three-dimensional structure of the same prot...

Embodiment 3

[0157] On the basis of the disclosure of the second embodiment, the present invention also discloses an embodiment, see Figure 5 , Figure 5 It is a flowchart of the method for predicting the three-dimensional structure of a protein provided in Example 3 of the present invention.

[0158] After using the parallel ant colony prediction method to obtain p optimal protein conformations, step S107 is also included: performing crossover on the p protein conformations to quickly obtain p crossover protein conformations. The crossover method is specifically:

[0159] Step S1071, randomly select two protein conformations M among the p optimal protein conformations bi and M bj is the parent conformation;

[0160] Step S1072, randomly in the parent conformation M bi and M bj Determine the position k, take the position k as the cut-off point, and set the parent conformation M bi cut into M bi k- and M bi K+ , the parent conformation M bj cut into M bj k- and M bj K+ ;

...

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Abstract

The invention provides a method for predicting a three-dimensional protein structure. The method comprises the steps of: a, selecting a target ant colony and initializing parameters of an ant colony algorithm; b, initializing protein conformation and establishing a mapping relationship between the protein conformation and a fragment library; c, optimizing the target ant colony under the guidance of pheromones by taking any one position on the protein conformation as a starting point, performing energy calculation on the optimized protein conformation, and selecting the protein conformation with the minimum energy; d, locally optimizing the protein conformation with the minimum energy, performing energy calculation, updating a pheromone matrix according to a calculation result, comparing the energy of the locally optimized protein conformation and the energy of the protein conformation with the minimum energy, and selecting the protein conformation with the minimum energy; e, repeating the steps c-d to obtain better protein conformation; and f, performing Loop reconstruction on the better protein conformation to obtain the optimal protein conformation. The invention further provides a device for predicting the three-dimensional protein structure.

Description

technical field [0001] The invention relates to the technical field of protein structure prediction, in particular to a method and device for predicting a three-dimensional protein structure. Background technique [0002] Biological studies have shown that proteins are composed of specific amino acid sequences. Normally, proteins do not exist as fully extended polypeptide chains, but as tightly folded three-dimensional structures, and the ability of a particular protein to perform its function is often determined by its three-dimensional structure. Therefore, determining the three-dimensional structure of a protein, or its conformation, is an important topic in the field of biology. [0003] At present, analytical chemistry methods such as X-ray diffraction and nuclear magnetic resonance have been used to analyze the three-dimensional structure of some proteins. However, these analytical techniques require a lot of time and cost, and cannot meet the needs of protein structu...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G06F19/14G16B10/00
Inventor 吕强
Owner SUZHOU UNIV
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