SAHG, a comprehensive database of predicted structures of all human proteins.
Most proteins from higher organisms are known to be multi-domain proteins and contain substantial numbers of intrinsically disordered (ID) regions. To analyse such protein sequences, those from human for instance, we developed a special protein-structure-prediction pipeline and accumulated the products in the Structure Atlas of Human Genome (SAHG) database at http://bird.cbrc.jp/sahg. With the pipeline, human proteins were examined by local alignment methods (BLAST, PSI-BLAST and Smith-Waterman profile-profile alignment), global-local alignment methods (FORTE) and prediction tools for ID regions (POODLE-S) and homology modeling (MODELLER). Conformational changes of protein models upon ligand-binding were predicted by simultaneous modeling using templates of apo and holo forms. When there were no suitable templates for holo forms and the apo models were accurate, we prepared holo models using prediction methods for ligand-binding (eF-seek) and conformational change (the elastic network model and the linear response theory). Models are displayed as animated images. As of July 2010, SAHG contains 42,581 protein-domain models in approximately 24,900 unique human protein sequences from the RefSeq database. Annotation of models with functional information and links to other databases such as EzCatDB, InterPro or HPRD are also provided to facilitate understanding the protein structure-function relationships.
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan. c-motono@aist.go.jp
Chie
C
Motono
Junichi
J
Nakata
Ryotaro
R
Koike
Kana
K
Shimizu
Matsuyuki
M
Shirota
Takayuki
T
Amemiya
Kentaro
K
Tomii
Nozomi
N
Nagano
Naofumi
N
Sakaya
Kiyotaka
K
Misoo
Miwa
M
Sato
Akinori
A
Kidera
Hidekazu
H
Hiroaki
Tsuyoshi
T
Shirai
Kengo
K
Kinoshita
Tamotsu
T
Noguchi
Motonori
M
Ota
D020134:Catalytic Domain; D030562:Databases, Protein; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D025941:Protein Interaction Mapping; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D014584:User-Computer Interface
D008024:Ligands; D011506:Proteins