Protein classification using comparative molecular interaction profile analysis system

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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)497-510
Number of pages14
JournalJournal of Bioinformatics and Computational Biology
Issue number3
Publication statusPublished - 2004 Sept
Externally publishedYes


  • CoMIPA
  • Interaction profile
  • Protein classification

ASJC Scopus subject areas

  • Medicine(all)
  • Cell Biology


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