title: Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment.
abstract: The community-wide GPCR Dock assessment is conducted to evaluate the status of molecular modeling and ligand docking for human G protein-coupled receptors. The present round of the assessment was based on the recent structures of dopamine D3 and CXCR4 chemokine receptors bound to small molecule antagonists and CXCR4 with a synthetic cyclopeptide. Thirty-five groups submitted their receptor-ligand complex structure predictions prior to the release of the crystallographic coordinates. With closely related homology modeling templates, as for dopamine D3 receptor, and with incorporation of biochemical and QSAR data, modern computational techniques predicted complex details with accuracy approaching experimental. In contrast, CXCR4 complexes that had less-characterized interactions and only distant homology to the known GPCR structures still remained very challenging. The assessment results provide guidance for modeling and crystallographic communities in method development and target selection for further expansion of the structural coverage of the GPCR universe.
authors.affiliation: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92039, USA.
authors.forename: Irina
authors.initials: I
authors.lastname: Kufareva
authors.forename: Manuel
authors.initials: M
authors.lastname: Rueda
authors.forename: Vsevolod
authors.initials: V
authors.lastname: Katritch
authors.forename: Raymond C
authors.initials: RC
authors.lastname: Stevens
authors.forename: Ruben
authors.initials: R
authors.lastname: Abagyan
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry; D011485:Protein Binding; D019718:Receptors, CXCR4 / Q000737:chemistry*; D050637:Receptors, Dopamine D3 / Q000737:chemistry*; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry*; D012457:Salicylamides / Q000737:chemistry; D013890:Thiourea / Q000031:analogs & derivatives / Q000737:chemistry
chemical_list: C527276:CXCR4 protein, human; D010446:Peptide Fragments; D019718:Receptors, CXCR4; D050637:Receptors, Dopamine D3; D043562:Receptors, G-Protein-Coupled; D012457:Salicylamides; D013890:Thiourea; C045989:eticlopride