Title

Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: Meeting new challenges

Authors

Irina Kufareva, Skaggs School of Pharmacy & Pharmaceutical Sciences
Vsevolod Katritch, Scripps Research Institute
Phil Biggin, University of Oxford Medical Sciences Division
Minsup Kim, Korea University
Kichul Park, Korea University
Sang Won Jung, Korea University
Art E. Cho, Korea University
Zara A. Sands, UCB S.A.
Liliana Ostopovici-Halip, UNM Health Sciences Center
Cristian G. Bologa, Academia Româna
Christoffer Norn, Københavns Universitet
Michal Brylinski, Louisiana State University
Jeffrey Skolnick, Georgia Institute of Technology
Henrik Keränen, Uppsala Universitet
Bart E. Lenselink, Leiden University
Gerard Van Westen, European Molecular Biology Laboratory
John P. Overington, European Molecular Biology Laboratory
Hugo Gutiérrez De Teráán, Uppsala Universitet
Vignir Isberg, Københavns Universitet
Kimberley M. Fidom, Københavns Universitet
Thomas M. Lehto, Københavns Universitet
David E. Gloriam, Københavns Universitet
Anirban Ghosh, Centre for Development of Advanced Computing, India
Uddhavesh Sonavane, Centre for Development of Advanced Computing, India
Rajendra Joshi, Centre for Development of Advanced Computing, India
Jie Xia, Peking University
Jui Hua Hsieh, National Institute of Environmental Health Sciences (NIEHS)
Liangren Zhang, Peking University
Xiang Simon Wang, Howard University
Horst Vogel, Ecole Polytechnique Fédérale de Lausanne
Shuguang Yuan, Ecole Polytechnique Fédérale de Lausanne
X. Feng, Baylor College of Medicine
M. Chen, Baylor College of Medicine
J. Ambia, Baylor College of Medicine

Document Type

Article

Publication Date

8-5-2014

Abstract

© 2014 Elsevier Ltd All rights reserved. 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.

Publication Source (Journal or Book title)

Structure

First Page

1120

Last Page

1139

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