Advanced tree-based kernels for protein classification

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

3 Citations (Scopus)

Abstract

One of the aims of modern Bioinformatics is to discover the molecular mechanisms that rule the protein operation. This would allow us to understand the complex processes involved in living systems and possibly correct dysfunctions. The first step in this direction is the identification of the functional sites of proteins. In this paper, we propose new kernels for the automatic protein active site classification. In particular, we devise innovative attribute-value and tree substructure representations to model biological and spatial information of proteins in Support Vector Machines. We experimented with such models and the Protein Data Bank adequately pre-processed to make explicit the active site information. Our results show that structural kernels used in combination with polynomial kernels can be effectively applied to discriminate an active site from other regions of a protein. Such finding is very important since it firstly shows a successful identification of catalytic sites for a very large family of proteins belonging to a broad class of enzymes.

Original languageEnglish
Title of host publicationAI IA 2007
Subtitle of host publicationArtificial Intelligence and Human-Oriented Computing - 10th Congress of the Italian Association for Artificial Intelligence, Proceedings
Pages218-229
Number of pages12
Publication statusPublished - 1 Dec 2007
Event10th Congress of the Italian Association for Artificial Intelligence, AI IA 2007 - Rome, Italy
Duration: 10 Sep 200713 Sep 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4733 LNAI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other10th Congress of the Italian Association for Artificial Intelligence, AI IA 2007
CountryItaly
CityRome
Period10/9/0713/9/07

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ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Cilia, E., & Moschitti, A. (2007). Advanced tree-based kernels for protein classification. In AI IA 2007: Artificial Intelligence and Human-Oriented Computing - 10th Congress of the Italian Association for Artificial Intelligence, Proceedings (pp. 218-229). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4733 LNAI).