Welcome to the GPCR Research Database
G protein-coupled receptors (GPCRs) comprise the largest family of integral membrane proteins. They are the most important class of drug targets. GPCR Research Database is designed to help GPCR research community build GPCR 3D structure models. There are three major parts of GPCRRD: (1) GPCR experimental restaint database. Although no solved X-ray or NMR structure is available for most GPCR sequences, numerous experiments have been performed on GPCRs to identify the critical residues and motifs. Experimental restraints were systematically collected from the literature using an automated text search algorithm combined with manual validation, with the purpose of assisting GPCR 3-D structure modeling and function annotation. (2) GPCR-I-TASSER server. The GPCR-I-TASSER algorithm is showed in the Figure. Given a GPCR sequence, LOMETS threading program was used to identify the putative related template structures in the PDB. For proteins of no significant template alignments, a novel ab initio transmembrane helix folding program was developed to build the 7 transmembrane bundles from scratch. Meanwhile, GPCRRD was searched for experimental restraints. Then we performed replica exchange Monte Carlo simulations to search the conformations space restricted by all the information above. The finally atomic structure model was rebuilt by FG-MD. There are four new developments compared to the original I-TASSER algorithm: improved force field for MC simulations, ab initio folding of transmembrane helix, GPCRRD experimental restraints and FG-MD refinement. (3) 3D atomic structures of 1028 putative GPCRs in the human genome were generated by GPCR-I-TASSER algorithm. Based on a benchmark test, all predicted models should have the correct folds (TM-score > 0.5) and share the characteristic seven-transmembrane helix topology. For questions and comments, please send email to firstname.lastname@example.org.
Links to other GPCR related databases:
- GPCRDB: information system for G protein-coupled receptors
- TinyGPAP Mutant Database
- GPCR-OKB: The G Protein Coupled Receptor Oligomerization Knowledge Base Project
- GPCR Natural Variants database
- GLIDA: GPCR ligand database
- IUPHAR GPCR database
- gpDB: G proteins and their interactions with GPCRs
- SEVENS: GPCR genes database
- Summary of activation changes in GPCR TMs
- List of all solved GPCRs in PDB library
J Zhang, Y Zhang, GPCRRD: G protein-coupled receptor spatial restraint database for 3-D structure modeling and function annotation Bioinformatics, 2010,26(23):3004-3005 doi: 10.1093/bioinformatics/btq563. (download the PDF file)
J Zhang, J Yang, R Jang, Y Zhang. GPCR-I-TASSER: A new hybrid approach to G protein-coupled receptor structure modeling with application to the human genome, submitted, 2014.