title: Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges.
abstract: Despite tremendous successes of GPCR crystallography, the receptors with available structures represent only a small fraction of human GPCRs. An important role of the modeling community is to maximize structural insights for the remaining receptors and complexes. The community-wide GPCR Dock assessment was established to stimulate and monitor the progress in molecular modeling and ligand docking for GPCRs. The four targets in the present third assessment round presented new and diverse challenges for modelers, including prediction of allosteric ligand interaction and activation states in 5-hydroxytryptamine receptors 1B and 2B, and modeling by extremely distant homology for smoothened receptor. Forty-four modeling groups participated in the assessment. State-of-the-art modeling approaches achieved close-to-experimental accuracy for small rigid orthosteric ligands and models built by close homology, and they correctly predicted protein fold for distant homology targets. Predictions of long loops and GPCR activation states remain unsolved problems.
authors: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92039, USA.
authors: Irina
authors: I
authors: Kufareva
authors: Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
authors: Vsevolod
authors: V
authors: Katritch
authors: Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA. Electronic address: stevens@scripps.edu.
authors: Raymond C
authors: RC
authors: Stevens
authors: Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92039, USA. Electronic address: rabagyan@ucsd.edu.
authors: Ruben
authors: R
authors: Abagyan
mesh_terms: D001665:Binding Sites / Q000235:genetics; D003461:Crystallography / Q000379:methods*; D006801:Humans; D008958:Models, Molecular; D008967:Molecular Biology / Q000379:methods*; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011487:Protein Conformation; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry* / Q000378:metabolism; D011985:Receptors, Serotonin / Q000737:chemistry
chemical_list: D043562:Receptors, G-Protein-Coupled; D011985:Receptors, Serotonin