Protein classification using comparative molecular interaction profile analysis system

Yoshiharu Hayashi*, Mime Kobayashi, Katsuyoshi Sakaguchi, Nao Iwata, Masaki Kobayashi, Yo Kikuchi, Yoshimasa Takahashi


研究成果: Article査読


We recently introduced a new molecular description factor, interaction profile Factor (IPF) that is useful for evaluating molecular interactions. IPF is a data set of interaction energies calculated by the Comparative Molecular Interaction Profile Analysis system (CoMIPA). CoMIPA utilizes AutoDock 3.0 docking program, and the system has shown to be a powerful tool in clustering the interacting properties between small molecules and proteins. In this report, we describe the application of CoMIPA for protein clustering. A sample set of 15 proteins that share less than 20% homology and have no common functional motifs in primary structure were chosen. Using CoMIPA, we were able to cluster proteins that bound to the same small molecule. Other structural homology-based clustering programs such as PSI-BLAST or PFAM were unable to achieve the same classification. The results are striking because it is difficult to find any common features in the active sites of these proteins that share the same ligand. CoMIPA adds new dimensions for protein classification and has the potential to be a helpful tool in predicting and analyzing molecular interactions.

ジャーナルJournal of Bioinformatics and Computational Biology
出版ステータスPublished - 2004 9月

ASJC Scopus subject areas

  • 医学一般
  • 細胞生物学


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