Analysis of evolutionary conservation patterns and their influence on identifying protein functional sites

Chun Fang*, Tamotsu Noguchi, Hayato Yamana

*この研究の対応する著者

研究成果: Article査読

3 被引用数 (Scopus)

抄録

Evolutionary conservation information included in position-specific scoring matrix (PSSM) has been widely adopted by sequence-based methods for identifying protein functional sites, because all functional sites, whether in ordered or disordered proteins, are found to be conserved at 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. Every value in PSSMs is calculated independently of each other, without carrying the contextual information of residues in the sequence. Therefore, adopting the direct output of PSSM for prediction fails to consider the relationship between conservation patterns of residues and the distribution of conservation scores in PSSMs. In order to demonstrate the importance of combining PSSMs with the specific conservation patterns of functional sites for prediction, three different PSSMbased methods for identifying three kinds of functional sites have been analyzed. Results suggest that, different PSSM-based methods differ in their capability to identify different patterns of functional sites, and better combining PSSMs with the specific conservation patterns of residues would largely facilitate the prediction.

本文言語English
論文番号1440003
ジャーナルJournal of Bioinformatics and Computational Biology
12
5
DOI
出版ステータスPublished - 2014 10 30

ASJC Scopus subject areas

  • 生化学
  • 分子生物学
  • コンピュータ サイエンスの応用

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