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Nucleic Acids Research, 2003, Vol. 31, No. 1 463-468
© 2003 Oxford University Press

Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species

Akihiro Yamaguchi, Mitsuo Iwadate1, Ei-ichiro Suzuki1, Kei Yura, Shigetsugu Kawakita1, Hideaki Umeyama*,1 and Mitiko Go

Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan 1 Department of Biomolecular Design, School of Pharmaceutical Sciences, Kitasato University, Tokyo 108-8641, Japan

*To whom correspondence should be addressed. Tel: +81 527892976; Fax: +81 527892977; Email: go{at}bio.nagoya-u.ac.jp
Correspondence may also be addressed to Hideaki Umeyama. Tel: +81 334469553; Fax: +81 334469553; Email: umeyamah{at}pharm.kitasato-u.ac.jp
Permanent address: Ei-ichiro Suzuki, Institute of Life Sciences, Ajinomoto Co., Inc., Ka-Building, 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki 210-8681, Japan
Present address: Kei Yura, Quantum Bioinformatics Group, Center for Promotion of Computational Science and Engineering, Japan Atomic Energy Research Institute, 8-1 Umemidai, Kizu-cho, Souraku-gun, Kyoto, 619-0215, Japan
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

ABSTRACT

Enlarged FAMSBASE is a relational database of comparative protein structure models for the whole genome of 41 species, presented in the GTOP database. The models are calculated by Full Automatic Modeling System (FAMS). Enlarged FAMSBASE provides a wide range of query keys, such as name of ORF (open reading frame), ORF keywords, Protein Data Bank (PDB) ID, PDB heterogen atoms and sequence similarity. Heterogen atoms in PDB include cofactors, ligands and other factors that interact with proteins, and are a good starting point for analyzing interactions between proteins and other molecules. The data may also work as a template for drug design. The present number of ORFs with protein 3D models in FAMSBASE is 183 805, and the database includes an average of three models for each ORF. FAMSBASE is available at http://famsbase.bio.nagoya-u.ac.jp/famsbase/.


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