Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment

Irina Kufareva, Manuel Rueda, Vsevolod Katritch, Raymond C. Stevens, Ruben Abagyan, Yasushi Yoshikawa, Toshio Furuya, Huisun Lee, Ambrish Roy, John Grime, Joseph Rebehmed, Yang Zhang, Luc Roumen, Iwan J.P. de Esch, Rob Leurs, Chris de Graaf, Youyong Li, Tingjun Hou, Michael M. Mysinger, Dahlia R. WeissJohn J. Irwin, Brian K. Shoichet, Fiona M. McRobb, Ben Capuano, Ian T. Crosby, David K. Chalmers, Elizabeth Yuriev, Qi Wang, Robert H. Mach, David E. Reichert, Gwo Yu Chuang, Didier Rognan, John Simms, Patrick Sexton, Denise Wootten, Dorota Latek, Umesh Ghoshdastider, Slawomir Filipek, LenServer, Andrea Kirkpatrick, Bartosz Trzaskowski, Adam Griffith, Soo Kyung Kim, Ravinder Abrol, William A. Goddard, Nagarajan Vaidehi, Alfonso Lam, Supriyo Bhattacharya, Hubert Li, Gouthaman Balaraman, Michiel Niesen, Sandeep Pal, Victor Solovyev, Yrii Vorobjev, Natalia Bakulina, Thijs Beuming, Stefano Costanzi, Lei Shi, Chris Higgs, Noeris Salam, Dmitry Lupyan, Woody Sherman, Feng Ding, Pradeep Kota, Srinivas Ramachandran, Nikolay V. Dokholyan, Jens Carlsson, Ryan G. Coleman, Hao Fan, Avner Schlessinger, John J. Irwin, Andrej Sali, Brian K. Shoichet, Irina Tikhonova, Irina Pogozheva, Andrei Lomize, Nathan E. Hall, Muhammad Muddassa, Yang Zhang, Ae Nim Pae, Jooyoung Lee, Laura Lopez, Cristian Obiol-Pardo, Jana Selent, Sadia Mahboob, Tim Werner, W. Bret Church, Michal Brylinski, Tadashi Ando, Aysam Guerler, Hongyi Zhou, Jeffrey Skolnick, Henri Xhaard, Wiktor Jurkowski, Arne Elofsson, Ahsan K. Murad, Malgorzata Drwal, Tom B. Dupree, Renate Griffith, Liliana Ostopovici-Halip, Cristian Bologa, K. M. Chen, J. Sun, Patrick Barth, Vladimir Yarov-Yarovoy, David Baker, Bas Vroling, Marijn P.A. Sanders, Sander B. Nabuurs, Gregory V. Nikiforovich

Research output: Contribution to journalArticle

229 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)1108-1126
Number of pages19
JournalStructure
Volume19
Issue number8
DOIs
StatePublished - Aug 10 2011

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Fingerprint Dive into the research topics of 'Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment'. Together they form a unique fingerprint.

  • Cite this

    Kufareva, I., Rueda, M., Katritch, V., Stevens, R. C., Abagyan, R., Yoshikawa, Y., Furuya, T., Lee, H., Roy, A., Grime, J., Rebehmed, J., Zhang, Y., Roumen, L., de Esch, I. J. P., Leurs, R., de Graaf, C., Li, Y., Hou, T., Mysinger, M. M., ... Nikiforovich, G. V. (2011). Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure, 19(8), 1108-1126. https://doi.org/10.1016/j.str.2011.05.012