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

Akihiro Yamaguchi, Mitsuo Iwadate, Ei Ichiro Suzuki, Kei Yura, Shigetsugu Kawakita, Hideaki Umeyama, Mitiko Go

Research output: Contribution to journalReview article

17 Citations (Scopus)

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 183805, and the database includes an average of three models for each ORF. FAMSBASE is available at http://famsbase.bio. nagoya-u.ac.jp/famsbase/.

Original languageEnglish
Pages (from-to)463-468
Number of pages6
JournalNucleic acids research
Volume31
Issue number1
DOIs
Publication statusPublished - 2003 Jan 1
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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    Yamaguchi, A., Iwadate, M., Suzuki, E. I., Yura, K., Kawakita, S., Umeyama, H., & Go, M. (2003). Enlarged FAMSBASE: Protein 3D structure models of genome sequences for 41 species. Nucleic acids research, 31(1), 463-468. https://doi.org/10.1093/nar/gkg117