Comparing kernels for predicting protein binding sites from amino acid sequence

Feihong Wu, Byron Olson, Drena Dobbs, Vasant Honavar

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

8 Scopus citations


The ability to identify protein binding sites and to detect specific amino acid residues that contribute to the specificity and affinity of protein interactions has important implications for problems ranging from rational drug design to analysis of metabolic and signal transduction networks. Support vector machines (SVM) and related kernel methods offer an attractive approach to predicting protein binding sites. An appropriate choice of the kernel function is critical to the performance of SVM. Kernel functions offer a way to incorporate domain-specific knowledge into the classifier. We compare the performance of three types of kernels functions: identity kernel, sequence-alignment kernel, and amino acid substitution matrix kernel in the case of SVM classifiers for predicting protein-protein, protein-DNA and protein-RNA binding sites. The results show that the identity kernel is quite effective in on all three tasks. The substitution kernel based on amino acid substitution matrices that take into account structural or evolutionary conservation or physicochemical properties of amino acids yields modest improvement.

Original languageEnglish (US)
Title of host publicationInternational Joint Conference on Neural Networks 2006, IJCNN '06
Number of pages5
StatePublished - 2006
EventInternational Joint Conference on Neural Networks 2006, IJCNN '06 - Vancouver, BC, Canada
Duration: Jul 16 2006Jul 21 2006

Publication series

NameIEEE International Conference on Neural Networks - Conference Proceedings
ISSN (Print)1098-7576


OtherInternational Joint Conference on Neural Networks 2006, IJCNN '06
CityVancouver, BC

All Science Journal Classification (ASJC) codes

  • Software


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