Analyzing conservation patterns and its influence on identifying protein functional

Chun Fang, Tamotsu Noguchi, Hayato Yamana

研究成果: Conference contribution

抄録

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.

本文言語English
ホスト出版物のタイトルProceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014
出版社International Society for Computers and Their Applications
ページ73-79
ページ数7
ISBN(印刷版)9781632665140
出版ステータスPublished - 2014 1 1
イベント6th International Conference on Bioinformatics and Computational Biology, BICOB 2014 - Las Vegas, NV, United States
継続期間: 2014 3 242014 3 26

出版物シリーズ

名前Proceedings of the 6th International Conference on Bioinformatics and Computational Biology, BICOB 2014

Conference

Conference6th International Conference on Bioinformatics and Computational Biology, BICOB 2014
国/地域United States
CityLas Vegas, NV
Period14/3/2414/3/26

ASJC Scopus subject areas

  • 情報システム
  • 健康情報学

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