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GPCRDock 2010 project and model-evaluation web site

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This community-wide GPCR Dock assessment was a collaboration between Stevens lab at TSRI, our lab and thirty five dedicated groups of modelers; it was based on two several structures of two GPCRs [2,3].

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.

Paper and Website

The paper has been published in Structure [1] ( Article, Supplementary materials ) and submitted models are served and evaluated from our lab model server. journal_cover

Bottomline

Here is the bottomline with a crescendo:

Publications

1. Kufareva I, Rueda M, Katritch V, Stevens RC, Abagyan R
Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment.
Structure, 2011 Aug 10, 19, 1108-26, 21827947

2. Wu B, Chien EY, Mol CD, Fenalti G, Liu W, Katritch V, Abagyan R, Brooun A, Wells P, Bi FC, Hamel DJ, Kuhn P, Handel TM, Cherezov V, Stevens RC
Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists.
Science, 2010 Nov 19, 330, 1066-71, 20929726

3. Chien EY, Liu W, Zhao Q, Katritch V, Han GW, Hanson MA, Shi L, Newman AH, Javitch JA, Cherezov V, Stevens RC.
Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist.
Science, 2010 Nov 19, 1091-5.

Last updated: 2013/05/31