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Hierarchical modeling method of protein side chain prediction

A modeling method and hierarchical technology, applied in special data processing applications, instruments, electrical digital data processing, etc.

Inactive Publication Date: 2013-05-08
HUZHOU TEACHERS COLLEGE
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

However, the commonly used side chain prediction methods often ignore this effect.

Method used

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  • Hierarchical modeling method of protein side chain prediction
  • Hierarchical modeling method of protein side chain prediction
  • Hierarchical modeling method of protein side chain prediction

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Experimental program
Comparison scheme
Effect test

Embodiment 1

[0062] The training data used is the same 850 proteins as the training set used by the Dunbrack library. These data were obtained by X-ray crystallography in the PDB library. If the PDB structure contains multiple chains, only the A chain is selected, and the similarity between any two chains is guaranteed not to exceed 50%.

[0063] The training process requires the following 8 types of data: residue type aa, secondary structure type ss, main chain torsion angle φ, main chain torsion angle ψ, side chain torsion angles x1, x2, x3, and x4. Before training, it is necessary to digitize the information and discretize the continuous data. The first is the protein type. At present, there are only 20 common amino acids involved in protein composition. Therefore, the protein type itself is discretized information, which is represented by integers 0-19. Similarly, the secondary structure of the main chain is also discrete information. There are only three kinds of protein secondary ...

Embodiment 2

[0072] The present invention employs three GPCR targets: 2RH1, 3EML and 3OE6. For these three experimental data, the hierarchical modeling method proposed by the present invention and the traditional non-hierarchical modeling method are respectively used to generate corresponding rotamer libraries, and then the quality of the rotamer libraries is compared. The comparison method is to count the number of angles whose x-angle difference between the residue candidate structure at a certain position in different rotamer libraries and the corresponding position in the natural structure is within 20°. As shown in table 2.

[0073] Table 2 Sampling results of hierarchical modeling method

[0074]

[0075]Among them, the two columns of x1 and x2 represent the statistical results for the corners of x1 and x2 respectively; x1+x2 represents the statistical results when x1 and x2 are satisfied at the same time. "Four layers" means the experimental results of the rotamer library gener...

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Abstract

The invention provides a hierarchical modeling method of protein side chain prediction. The hierarchical modeling method of the protein side chain prediction comprises the following steps: (1) taking main chain information as input, executing a first layer reasoning unit, outputting a side chain torsion angle X1, (2) taking the main chain information and the side chain torsion angle X1 as input, executing a second layer reasoning unit, outputting a side chain torsion angle X2, (3) taking the main chain information, the side chain torsion angle X1 and the side chain torsion angle X2 as input, executing a third layer reasoning unit, outputting a side chain torsion angle X3, and (4) taking the main chain information, the side chain torsion angle X1, the side chain torsion angle X2 and the side chain torsion angle X3 as input, and executing a forth layer reasoning unit, outputting a side chain torsion angle X4. The invention further provides a practice process of the hierarchical modeling method for all the layer reasoning units based on the hierarchical modeling method. Meanwhile, for all the layer reasoning units and combining data bank network (DBN) models corresponding to all the layer reasoning units output by the practice process, the invention further provides a sampling process of the hierarchical modeling method.

Description

technical field [0001] The invention relates to the technical field of protein structure prediction, in particular to a hierarchical modeling method for protein side chain prediction. Background technique [0002] The protein side chain (Side-chain) spatial structure is an important factor affecting the protein molecular structure and function. On the one hand, there are great differences in the composition of the "R" group of different amino acid residues; The "R" group will also assume a different conformation. The specific structural state of the "R" group of an amino acid residue is usually called the rotamer (rotational isomer, or rotamer) of the residue. To facilitate side chain prediction, torsion angles (or dihedral angles) of chemical bonds are usually used to describe rotamers. In addition to the dihedral angles φ, ψ, and ω of the part (main chain) involved in the formation of peptide bonds in the amino acid residues, there are 0 to 4 dihedral angles ranging fro...

Claims

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Application Information

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IPC IPC(8): G06F19/12
Inventor 蒋云良黄旭吕强缪大俊钱培德范婧
Owner HUZHOU TEACHERS COLLEGE
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