SAHG, a comprehensive database of predicted structures of all human proteins

Abstract

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.

Proteome-wide prediction of targets for aspirin: new insight into the molecular mechanism of aspirin

“…The first source is the Protein Data Bank managed by Research Collaboratory for Structural Bioinformatics (RCSB PDB) ( ) ( Rose et al, 2011 ), which contains 6,983 structures of human proteins. The other two repositories are structure models built by homology modeling techniques from Structure Atlas of Human Genome ( Motono et al, 2011 ) ( ) and GPCR Research Database (GPCR-RD) ( Zhang & Zhang, 2010 ), which have 16,529 and 1,028 structures, respectively. This procedure yielded a total of 24,540 human protein structures.…”

Peer Review #4 of "Proteome-wide prediction of targets for aspirin: new insight into the molecular mechanism of aspirin (v0.1)"

“…The first source is the Protein Data Bank managed by Research Collaboratory for Structural Bioinformatics (RCSB PDB) (http://www.rcsb.org) (Rose et al 2011), which contains 6983 structures of human proteins. The other two repositories are structure models built by homology modeling techniques from Structure Atlas of Human Genome (Motono et al 2011) PeerJ reviewing PDF | (2015:12:7990:2:0:NEW 18 Feb 2016)…”

“…Our query database contains totally 17425 non-redundant structures of human protein from three sources: RCSB PDB database(Rose et al 2011), Structure atlas of human genome (SAHG)(Motono et al 2011) and GPCR Research Database (GPCRRD)(Zhang & Zhang 2010). With the increase number of crystal structures in the future, other new targets of aspirin may be identified.…”

Simplified Swarm Optimization-Based Function Module Detection in Protein–Protein Interaction Networks

“…Available data on PPI are greatly enriched because of the fast development of high-throughput screening [7] and data mining technologies [8]. Some widely used and most complete open datasets are also released, for instance, the Biomolecular Interaction Network Database (BIND) [9], Database of Interaction Proteins (DIP) [10], IntAct [11], Human Protein Reference Database (HPRD) [12], and Molecular Interaction Database (MINT) [13,14].…”