A Gaussian evolutionary method for predicting protein-protein interaction sites

Kang Ping Liu, Jinn-Moon Yang*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Protein-protein interactions play a pivotal role in modern molecular biology. Identifying the protein-protein interaction sites is great scientific and practical interest for predicting protein-protein interactions. In this study, we proposed a Gaussian Evolutionary Method (GEM) to optimize 18 features, including ten atomic solvent and eight protein 2nd structure features, for predicting protein-protein interaction sites. The training set consists of 104 unbound proteins selected from PDB and the predicted successful rate is 65.4% (68/104) proteins in the training dataset. These 18 parameters were then applied to a test set with 50 unbound proteins. Based on the threshold obtained from the training set, our method is able to predict the binding sites for 98% (49/50) proteins and yield 46% successful prediction and 42.3% average specificity. Here, a binding-site prediction is considered successful if 50% predicted area is indeed located in protein-protein interface (i.e. the specificity is more than 0.5). We believe that the optimized parameters of our method are useful for analyzing protein-protein interfaces and for interfaces prediction methods and protein-protein docking methods.

Original languageEnglish
Title of host publicationEvolutionary Computation, Machine Learning and Data Mining in Bioinformatics - 5th European Conference, EvoBIO 2007, Proceedings
Pages143-154
Number of pages12
StatePublished - 1 Dec 2007
Event5th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, EvoBIO 2007 - Valencia, Spain
Duration: 11 Apr 200713 Apr 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4447 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference5th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, EvoBIO 2007
CountrySpain
CityValencia
Period11/04/0713/04/07

Keywords

  • Atomic solvation parameter
  • Gaussian evolutionary method
  • Protein-protein binding site
  • Protein-protein interactions

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  • Cite this

    Liu, K. P., & Yang, J-M. (2007). A Gaussian evolutionary method for predicting protein-protein interaction sites. In Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics - 5th European Conference, EvoBIO 2007, Proceedings (pp. 143-154). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4447 LNCS).