Protein kinase specificity prediction method and device based on nearest neighbor algorithm

A protein kinase and prediction method technology, applied in the field of protein modification site recognition, can solve the problems of low sensitivity and specificity prediction accuracy, and achieve the effect of improving sensitivity and specificity, and increasing accuracy

Inactive Publication Date: 2014-04-23
SHENZHEN INST OF ADVANCED TECH
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0006] The purpose of the present invention is to overcome the above disadvantages, provide a protein kinase specificity prediction method based on the nearest neighbor algorithm, and solve the technical problems of low sensitivity, specificity and low prediction accuracy in the prior art

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  • Protein kinase specificity prediction method and device based on nearest neighbor algorithm
  • Protein kinase specificity prediction method and device based on nearest neighbor algorithm
  • Protein kinase specificity prediction method and device based on nearest neighbor algorithm

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Embodiment 1

[0051] Embodiment 1 of the present invention provides a protein kinase specificity prediction method based on the nearest neighbor algorithm, which is used to mark the phosphorylation sites of different protein kinase families, such as figure 1 As shown, the method includes the following steps:

[0052] Step S101: extract protein kinase-specific phosphorylation site data from the phosphorylation database, and construct a data set for kinase identification;

[0053] In this example, the phosphorylation database is Phospho.ELM9.0.

[0054] Step S102: removing phosphorylation site data that does not include protein kinase information from the data set used for kinase identification, and merging duplicate data to remove redundancy;

[0055] Step S103: Extract phosphorylation site peptide data for each phosphorylation site in the data set, the phosphorylation site peptide is centered on the phosphorylation site, including upstream and downstream of the phosphorylation site n amin...

Embodiment 2

[0070] Embodiment 2 of the present invention provides a device for predicting protein kinase specificity based on the nearest neighbor algorithm, which is used to mark the phosphorylation sites of different protein kinase families, such as figure 2 As shown, the device includes: a database extraction module 100 , a preprocessing module 200 , a phosphorylated peptide generation module 300 , a data set generation module 400 , a sequence comparison module 500 and an evaluation module 600 .

[0071] Wherein, the database extraction module 100 is used to extract protein kinase-specific phosphorylation site data from the phosphorylation database, and constructs a data set for kinase identification; the preprocessing module 200 is used for kinase identification constructed by the database extraction module. Phosphorylation site data that does not include protein kinase information is removed from the data set; and duplicate data is merged to remove redundancy; the phosphorylated pept...

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Abstract

The invention relates to the technical field of protein modification site identification, in particular to a protein kinase specificity prediction method and device based on a nearest neighbor algorithm. According to the prediction method, amino acid information on the upstream and the downstream of a phosphorylation site is fully utilized, and the accuracy of prediction is increased. According to the protein kinase specificity prediction method, an amino acid permutation matrix is used for scoring the similarity of a phosphorylation site peptide fragment to be detected and a known phosphorylation site peptide fragment, the phosphorylation site peptide fragment to be detected is marked to be the highest scored known phosphorylation site peptide fragment, and the sensitivity and the specificity of prediction are improved.

Description

【Technical field】 [0001] The invention relates to the technical field of protein modification site recognition, in particular to a protein kinase specificity prediction method and device based on the nearest neighbor algorithm. 【Background technique】 [0002] Protein phosphorylation and dephosphorylation play an important role in a variety of eukaryotic cells, such as regulating almost all life activities such as cell signal transduction, cell differentiation, cell growth, and cell apoptosis. Protein kinases (PKS) catalyze specific receptor amino acids in protein substrates, and each kinase only catalyzes specific substrates. Protein phosphorylation sites mainly occur at tyrosine (Y), serine (S) and threonine (T) residues (Wu et al., J Proteome Res, 2007, 6(5):1812). Abnormal protein phosphorylation often leads to abnormal cell life activities, and even cell damage or cell canceration (Yang et al., J Proteome Res, 2006, 5(5): 252). Therefore, understanding the phosphorylat...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/18
Inventor 周丰丰赵苗苗张召罗幼喜麦国琴
Owner SHENZHEN INST OF ADVANCED TECH
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