Enlarged FAMSBAS; Protein 3D structure models of genome sequences for 41 species

Yamaguchi, Akihiro*; Iwadate, Mitsuo*; Suzuki, Eiichiro*; Yura, Kei; Kawakita, Shigetsune*; Umeyama, Hideaki*; Go, Michiko*

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 FAMS, Full Automatic Modeling System. Enlarged FAMSBASE provides a wide range of query keys, such as name of ORF (open reading frame), ORF keywords, 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/.