TY - JOUR
T1 - Enlarged FAMSBASE
T2 - Protein 3D structure models of genome sequences for 41 species
AU - Yamaguchi, Akihiro
AU - Iwadate, Mitsuo
AU - Suzuki, Ei Ichiro
AU - Yura, Kei
AU - Kawakita, Shigetsugu
AU - Umeyama, Hideaki
AU - Go, Mitiko
N1 - Funding Information:
This work was supported by a Grant-in-Aid for Scientific Research on Priority Area (C), Genome Information Science from the Ministry of Education, Culture, Sports, Science and Technology of Japan. The authors are grateful to Dr. Ken Nishikawa of NIG for the gift of genome sequence information of 41 species processed through PSI-BLAST analysis against amino acid sequences of proteins in PDB.
PY - 2003/1/1
Y1 - 2003/1/1
N2 - 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/.
AB - 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/.
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U2 - 10.1093/nar/gkg117
DO - 10.1093/nar/gkg117
M3 - Review article
C2 - 12520053
AN - SCOPUS:0037250367
SN - 0305-1048
VL - 31
SP - 463
EP - 468
JO - Nucleic acids research
JF - Nucleic acids research
IS - 1
ER -