Method for determining interaction between proteins based on random projection integrated classification
A technology of random projection and measurement method, applied in the field of biology, can solve the problems of not meeting the technical development requirements, high false positive rate, low efficiency, etc., and achieve the effects of excellent measurement stability, precise expression, and excellent accuracy
Inactive Publication Date: 2018-01-19
LANZHOU JIAOTONG UNIV +1
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Problems solved by technology
Although the existing technology has disclosed the method of biotechnology to obtain PPIs data from organisms, the existing technology has the disadvantages of low efficiency, high cost and high false positive rate, which obviously does not meet the requirements of technological development. It is urgent to develop a method with high efficiency and low cost. Low methods and techniques for determining PPIs
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[0028] A method for determining the interaction between proteins based on random projection integrated classification, characterized in that it comprises the following steps:
[0029] A. Protein data screening
[0030] Screen protein interaction pairs from the protein database DIP;
[0031] B. Substitution Matrix Representation
[0032] Using BLOSUM62 matrix, a protein sequence of length N will generate an N×20 matrix, and the SMR matrix represents the expression: SMR(i,j)=B(P(i),j) i=1...N,j =1...20,
[0033] B(P(i), j) represents the probability that amino acid i is mutated into amino acid j, and P(i), j represents the protein sequence position composed of N amino acids;
[0034] C. Discrete cosine transform
[0035] The discrete cosine transform DCT formula is as follows:
[0036]
[0037] in,
[0038] D. Establish a random projection ensemble model
[0039] Select the original matrix X of n×d dimensions n×d , the original matrix is mapped to obtain a low-dim...
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The invention relates to the field of biology and particularly relates to a method for determining the interaction between proteins based on random projection integrated classification. The method comprises A, protein data screening, B, substitution matrix characterization, C, discrete cosine transformation, D, establishment of random projection integrated model and E, model determination. The method can acquire a prediction model of interaction between proteins according to classification characteristics of interaction between proteins and the prediction model is used for detecting interaction between proteins related to diseases so that the problem that the prior art cannot predict interaction between proteins and disease correlation and prediction of interaction between proteins and disease correlation is realized. The method is suitable for screening animal and strain protein pairs, builds a random projection integrated model for later analysis through substitution matrix characterization and discrete cosine transformation and provides accurate effect display and expression. Compared with the traditional method, the method provided by the invention has the better accuracy rate,sensitivity, a positive predictive value and stability and accuracy of Matthews correlation coefficient measurement.
Description
technical field [0001] The invention relates to the field of biology, in particular to a method for measuring the interaction between proteins based on random projection integrated classification. Background technique [0002] Protein-protein interactions (PPIs) are the result of interactions in a certain time and space, are the basis for realizing protein functions, and are the key to studying cell life activities. Although the existing technology has disclosed the method of biotechnology to obtain PPIs data from organisms, the existing technology has the disadvantages of low efficiency, high cost and high false positive rate, which obviously does not meet the requirements of technological development. It is urgent to develop a method with high efficiency and low cost. Low methods and techniques for measuring PPIs. Contents of the invention [0003] The invention solves the deficiencies of the prior art and provides a protein-protein interaction assay method based on ran...
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Login to View More IPC IPC(8): G01N33/68G06F19/12G06F19/18
Inventor 宋晓宇邱泽阳孙向阳赵阳
Owner LANZHOU JIAOTONG UNIV