Title

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

Authors

Irina Kufareva, Skaggs School of Pharmacy & Pharmaceutical Sciences
Manuel Rueda, Skaggs School of Pharmacy & Pharmaceutical Sciences
Vsevolod Katritch, Skaggs School of Pharmacy & Pharmaceutical Sciences
Raymond C. Stevens, Scripps Research Institute
Ruben Abagyan, Skaggs School of Pharmacy & Pharmaceutical Sciences
Yasushi Yoshikawa, PharmaDesign, Inc.
Toshio Furuya, PharmaDesign, Inc.
Huisun Lee, University of Michigan, Ann Arbor
Ambrish Roy, University of Michigan, Ann Arbor
John Grime, University of Michigan, Ann Arbor
Joseph Rebehmed, University of Michigan, Ann Arbor
Yang Zhang, University of Michigan, Ann Arbor
Luc Roumen, Vrije Universiteit Amsterdam
Iwan J.P. de Esch, Vrije Universiteit Amsterdam
Rob Leurs, Vrije Universiteit Amsterdam
Chris de Graaf, Vrije Universiteit Amsterdam
Youyong Li, Soochow University
Tingjun Hou, Soochow University
Michael M. Mysinger, University of California, San Francisco
Dahlia R. Weiss, University of California, San Francisco
John J. Irwin, University of California, San Francisco
Brian K. Shoichet, University of California, San Francisco
Fiona M. McRobb, Monash Institute of Pharmaceutical Sciences
Ben Capuano, Monash Institute of Pharmaceutical Sciences
Ian T. Crosby, Monash Institute of Pharmaceutical Sciences
David K. Chalmers, Monash Institute of Pharmaceutical Sciences
Elizabeth Yuriev, Monash Institute of Pharmaceutical Sciences
Qi Wang, Washington University School of Medicine in St. Louis, Mallinckrodt Institute of Radiology
Robert H. Mach, Washington University School of Medicine in St. Louis, Mallinckrodt Institute of Radiology
David E. Reichert, Washington University School of Medicine in St. Louis, Mallinckrodt Institute of Radiology
Gwo Yu Chuang, Université de Strasbourg
Didier Rognan, Université de Strasbourg
John Simms, Monash University
Patrick Sexton, Monash University

Document Type

Article

Publication Date

8-10-2011

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. © 2011 Elsevier Ltd. All rights reserved.

Publication Source (Journal or Book title)

Structure

First Page

1108

Last Page

1126

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