Analyzing conservation patterns and its influence on identifying protein functional

Chun Fang, Tamotsu Noguchi, Hayato Yamana

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

    Abstract

    Evolutionary conservation information included in position-specific scoring matrix (PSSM) has been adopted by almost all sequence-based methods for identifying protein functional sites, because all functional sites, whether in ordered or disordered proteins, are found to be conserved to some extent. However, different functional sites have different conservation patterns, some of them are linear contextual, some of them are mingled with highly variable residues, and some others seem to be conserved independently. All existing studies used the direct output of PSSM for functional sites prediction, without considering the relationship between conservation patterns of residues and the distribution of conservation scores in PSSMs. In order to demonstrate the importance of analyzing conservation patterns, three PSSM-based methods for identifying 3 kinds of functional sites have been compared. Experiment results show that, although all the methods are based on the same feature - PSSM of protein sequence, they are competent in identifying different patterns of functional sites: the PSSM-based method is competent for identifying functional site which is independently conserved; the smoothed-PSSM is competent for identifying functional site which is continuous conserved; and the masked-smoothed- PSSM based method is competent for identifying functional site which is mingled with intensively highly flexible and highly conserved residues.

    Original languageEnglish
    Title of host publicationProceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014
    PublisherInternational Society for Computers and Their Applications
    Pages73-79
    Number of pages7
    ISBN (Print)9781632665140
    Publication statusPublished - 2014
    Event6th International Conference on Bioinformatics and Computational Biology, BICOB 2014 - Las Vegas, NV
    Duration: 2014 Mar 242014 Mar 26

    Other

    Other6th International Conference on Bioinformatics and Computational Biology, BICOB 2014
    CityLas Vegas, NV
    Period14/3/2414/3/26

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    ASJC Scopus subject areas

    • Information Systems
    • Health Informatics

    Cite this

    Fang, C., Noguchi, T., & Yamana, H. (2014). Analyzing conservation patterns and its influence on identifying protein functional. In Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014 (pp. 73-79). International Society for Computers and Their Applications.