Structure, Volume 19, Issue 8, 2011

Summary

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.

D3/eticlopride

A small molecule in a small pocket with two good template structures available

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CXCR4/IT1t

A small molecule in a large pocket designed for peptide binding with distant templates available

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CXCR4/CVX15

A peptide-analogue in a pocket with distant templates available

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