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Detection of cleavage sites for HIV-1 protease in native proteins
Halmstad University, School of Information Science, Computer and Electrical Engineering (IDE), Halmstad Embedded and Intelligent Systems Research (EIS).
2006 (English)In: Proceedings of LSS Computational Systems Bioinformatics Conference: Computational Systems Bioinformatics Conference (vol. 5), Imperial College Press, 2006, 249-256 p.Conference paper, (Refereed)
Abstract [en]

Predicting novel cleavage sites for HIV-1 protease in non-viral proteins is a difficult task because of the scarcity of previous cleavage data on proteins in a native state. We introduce a three-level hierarchical classifier which combines information from experimentally verified short oligopeptides, secondary structure and solvent accessibility information from prediction servers to predict potential cleavage sites in non-viral proteins. The best classifier using secondary structure information on the second level classification of the hierarchical classifier is the one using logistic regression. By using this level of classification, the false positive ratio was reduced by more than half compared to the first level classifier using only the oligopeptide cleavage information. The method can be applied on other protease specificity problems too, to combine information from oligopeptides and structure from native proteins.

Place, publisher, year, edition, pages
Imperial College Press, 2006. 249-256 p.
Keyword [en]
Bayes Theorem, Binding Sites, Cluster Analysis, Computational Biology, HIV Protease, HIV-1, Oligopeptides, Peptides
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:hh:diva-2121Scopus ID: 2-s2.0-34250823439Local ID: 2082/2516OAI: oai:DiVA.org:hh-2121DiVA: diva2:239339
Conference
LSS Computational Systems Bioinformatics Conference
Available from: 2008-11-11 Created: 2008-11-11 Last updated: 2014-05-06Bibliographically approved

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CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf