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Protein and micromolecule binding site predicting method and predicting device

A technology combining sites and prediction methods, applied in proteomics, ICT adaptation, genomics, etc., can solve the problem of limited prediction effect, and achieve the effect of good characterization effect and good prediction effect.

Active Publication Date: 2019-09-10
HENAN NORMAL UNIV
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Problems solved by technology

However, when the algorithm constructs the prediction model and calculates, it often only pays attention to the properties of a single amino acid residue, and does not consider the overall position, so its prediction effect is relatively limited

Method used

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  • Protein and micromolecule binding site predicting method and predicting device
  • Protein and micromolecule binding site predicting method and predicting device
  • Protein and micromolecule binding site predicting method and predicting device

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Embodiment Construction

[0047] The present invention will be further described in detail below in conjunction with specific embodiments.

[0048] Example 1 of the method for predicting binding sites of proteins and small molecules

[0049] In the present invention, a new method for predicting the binding sites of small molecules and proteins based on the PDB data of protein small molecules is proposed. The classification model constructed in the experiments of the present invention can be used to predict binding sites and non-binding sites. By extracting features such as the physicochemical properties and evolution information of residues on the protein sequence, generate the data sets required for training and testing, train and test the classification model, and finally use the classification model to classify and predict the binding sites and non-binding sites of proteins point. Protein PSSM matrix information has been used by many scientists, such as predicting binding sites, secondary structure...

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Abstract

The invention relates to a protein and micromolecule binding site predicting method and a predicting device, wherein the method and the device belong to the field of micromolecule binding site predicting technology. The invention provides the new protein and micromolecule binding site predicting method. In the method, a sliding sampling window method is used for extracting data. A protein bindingfunction is affect by a binding residue surrounding environment. Therefore the sampling window method is used for extracting data for representing the characteristic of the residue at the central position, thereby realizing better representing effect. After an XGBoost classification model is constructed by means of the extracted characteristic, the classification model has better predicting effect, and the binding site between the protein and the micromolecule can be more accurately predicted.

Description

technical field [0001] The invention relates to a prediction method and a prediction device for binding sites of proteins and small molecules, and belongs to the technical field of prediction of binding sites of small molecule binding proteins. Background technique [0002] Proteins do not exist independently, they have to interact with such as DNA, RNA and other proteins and small molecules to exert their biological functions. Among them, the protein-small molecule binding site is the active site on the surface of the protein that performs the biological function of the protein. Knowing the interaction site between the protein and other small molecules can also help scientists understand more about the biological function of the protein and provide a basis for the development of protein drugs. Design provides technical support. [0003] Usually, people can find the binding sites of small molecules on the surface of proteins through biological experiments, and the binding s...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/30
CPCG16B20/30Y02A90/10
Inventor 王伟李克亮张仕光吕贺贺赵远
Owner HENAN NORMAL UNIV
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