VISCANA: Visualized cluster analysis of protein - Ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening

Shinji Amari, Masahiro Aizawa, Junwei Zhang, Kaori Fukuzawa, Yuji Mochizuki, Yoshio Iwasawa, Kotoko Nakata, Hiroshi Chuman, Tatsuya Nakano

研究成果: Article査読

108 被引用数 (Scopus)

抄録

We have developed a visualized cluster analysis of protein - ligand interaction (VISCANA) that analyzes the pattern of the interaction of the receptor and ligand on the basis of quantum theory for virtual ligand screening. Kitaura et al. (Chem. Phys. Lett. 1999, 572, 319-324.) have proposed an ab initio fragment molecular orbital (FMO) method by which large molecules such as proteins can be easily treated with chemical accuracy. In the FMO method, a total energy of the molecule is evaluated by summation of fragment energies and interfragment interaction energies (IFIEs). In this paper, we have proposed a cluster analysis using the dissimilarity that is defined as the squared Euclidean distance between IFIEs of two ligands. Although the result of an ordered table by clustering is still a massive collection of numbers, we combine a clustering method with a graphical representation of the IFIEs by representing each data point with colors that quantitatively and qualitatively reflect the IFIEs. We applied VISCANA to a docking study of pharmacophores of the human estrogen receptor a ligand-binding domain (57 amino acid residues). By using VISCANA, we could classify even structurally different ligands into functionally similar clusters according to the interaction pattern of a ligand and amino acid residues of the receptor protein. In addition, VISCANA could estimate the correct docking conformation by analyzing patterns of the receptor-ligand interactions of some conformations through the docking calculation.

本文言語English
ページ(範囲)221-230
ページ数10
ジャーナルJournal of chemical information and modeling
46
1
DOI
出版ステータスPublished - 2006
外部発表はい

ASJC Scopus subject areas

  • 化学 (全般)
  • 化学工学(全般)
  • コンピュータ サイエンスの応用
  • 図書館情報学

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