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Protein complex recognizing method based on range estimation

A technology of protein complexes and recognition methods, applied in special data processing applications, instruments, electrical digital data processing, etc., can solve problems such as insurmountable efficiency

Inactive Publication Date: 2008-08-20
CENT SOUTH UNIV
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  • Abstract
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Problems solved by technology

Since CFinder needs to enumerate all the maximal clusters in the network, its efficiency becomes an insurmountable bottleneck for relatively large-scale networks

Method used

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  • Protein complex recognizing method based on range estimation
  • Protein complex recognizing method based on range estimation
  • Protein complex recognizing method based on range estimation

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Embodiment Construction

[0020] 1. Statistical analysis of topological features of known protein complexes

[0021] The most widely studied species is yeast, and there are already a number of experimentally determined yeast protein complexes. The present invention downloads the known yeast protein complex and yeast protein interaction network data from the MIPS (Munich Information center for Protein Sequences) database. The interaction data were removed from self-interactions and redundant interactions, and the final protein interaction network consisted of 4546 yeast proteins and 12319 pairs of interactions. The average clustering coefficient of the entire network is 0.4, the network diameter is 13, and the characteristic path length (ie, the average value of the shortest path length between any two vertices in the network) is 4.42. The protein complex data set has a total of 216 after removing complexes with only one protein. The smallest complex includes 2 proteins, the largest complex includes 81...

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Abstract

The invention discloses a protein compound recognition method based on the range estimation, which takes the most short distance between protein apexes as a key parameter to recognize the protein compound, and controls the dense degree of the recognized the protein compound by the function probability between the protein apexes and the protein compound based on finding that the most short distance between the protein apexes in the known protein compound generally does not surpass 2. The realization of the invention is simply; a plurality of known proteins compound with the biological significance can be recognized through the protein interaction network, the invention has the very good toughness for the high proportion false positive and false negative which universally exist in the protein interaction large-scale data, and solves the chemical experiment cost to be expensive and the biology difficult problems that the quantity of single recognition is small and the dynamic compound is very difficult to recognized effectively.

Description

technical field [0001] The invention belongs to the field of system biology, and in particular relates to the identification of protein complexes. Background technique [0002] In the post-genome era, systematic analysis and comprehensive understanding of biological network topology and intracellular biochemical processes have become a very important research topic. Each protein in the cell does not complete the assigned function independently, but forms a large complex by interacting with other proteins, and completes a specific function in a specific time and space, and the function of some proteins is only in the complex It can only be played out after it is formed. Identifying these protein complexes plays an important role in predicting protein function and explaining specific biological processes. [0003] Currently, methods for identifying protein complexes include chemical experimental assays, species comparison methods based on evolutionary models, analysis method...

Claims

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Application Information

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IPC IPC(8): G06F19/00G06F19/12
Inventor 王建新李敏
Owner CENT SOUTH UNIV
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