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Protein folding optimizing method based on ant group algorithm

A technology of protein folding and optimization method, applied in the field of protein folding optimization using ant colony algorithm, to achieve the effect of fast and effective solution

Inactive Publication Date: 2008-08-06
SUN YAT SEN UNIV
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  • Abstract
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  • Claims
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Problems solved by technology

[0004] Except for some special protein sequences, the protein folding problem is an NP-complete problem, which means that the problem cannot be solved in polynomial computing time.

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  • Protein folding optimizing method based on ant group algorithm
  • Protein folding optimizing method based on ant group algorithm
  • Protein folding optimizing method based on ant group algorithm

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Embodiment Construction

[0034] The method of the invention will be further described below in conjunction with the accompanying drawings.

[0035] There are a total of twenty amino acids in nature. Using different classification methods, they can be classified as acidic, basic or neutral; positively charged, negatively charged or uncharged; hydrophobic or hydrophilic and so on. For globular proteins in aqueous solution, its hydrophilic amino acids tend to distribute on the surface of the sphere due to the attraction of water molecules. Since hydrophobic amino acids are repelled by water molecules, except for some special hydrophobic amino acid regions distributed on the surface, most of the remaining hydrophobic amino acids will gather in the interior of the globular protein to form a core.

[0036] Some two-dimensional HP fold structures of protein sequences containing 48 amino acids are shown in Fig. 1, where solid squares represent hydrophobic amino acids and open squares represent hydrophilic ami...

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Abstract

The invention discloses a protein folding optimizing method based on an ant colony algorithm. The method comprises the following steps that: firstly, ants are arranged in a left initial square grid and a right initial square grid by using a hydrophobic-polar model; then, amino acids in the protein are arranged into grids by the ants according to a pheromone and heuristic information, updating of the local pheromone is executed while the ants make a movement, if an occurrence of stasis occurs, a maintenance is performed to a corresponding pathway; finally, after all the ants complete a construction for protein folding pathways, updating for the global pheromone is executed. A protein structure with smallest free energy can be obtained by constantly repeating the steps. Compared with the prior algorithm for solving the problem of protein folding, the protein folding optimizing method provided by the invention has the advantages of high efficiency, quickness, etc.

Description

Technical field: [0001] The invention relates to two major fields of biological information technology and intelligent computing, and mainly relates to a method for optimizing protein folding by using an ant colony algorithm. technical background: [0002] The function of proteins and their structure are closely linked, and the most important step in protein analysis is to find out the protein structure. In nature, proteins in aqueous solution fold naturally to their native structure in a very short period of time. Although existing experimental techniques, such as X-ray crystallography, nuclear magnetic resonance, protein engineering, mass spectrometry, fluorescence resonance energy transfer, and atomic force microscopy, can be used to generate images of proteins, they are generally expensive and time-consuming. More importantly, each experimental technique has its own different application limitations. Since many simple protein sequences have only a unique native structu...

Claims

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Application Information

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IPC IPC(8): G06N3/00
Inventor 张军胡晓敏黄韬
Owner SUN YAT SEN UNIV
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