Enlarged FAMSBASE: Protein 3D Structure Models of Genome Sequences for 41 Species

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2003 Jan 10

PMID 12520053

Citations 5

Authors

Akihiro Yamaguchi

Mitsuo Iwadate

Ei-Ichiro Suzuki

Kei Yura

Shigetsugu Kawakita

Hideaki Umeyama

Mitiko Go

Affiliations

Soon will be listed here.

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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