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J Chem Inf Model. 2014 Aug 25;54(8):2243-54. doi: 10.1021/ci5002857. Epub 2014 Jul 31.

Alternative quality assessment strategy to compare performances of GPCR-ligand docking protocols: the human adenosine A(2A) receptor as a case study.

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Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova , via Marzolo 5, 35131 Padova, Italy.


The progress made in the field of G protein-coupled receptors (GPCRs) structural determination has increased the adoption of docking-driven approaches for the identification or optimization of novel potent and selective ligands. In this work, we compared the performances of the 16 different docking/scoring combinations using the recently released crystal structures of the human A2A AR (hA2A AR) in complex with both agonists and antagonists. The proposed evaluation strategy encompasses the use of three complementary "quality descriptors": (a) the number of conformations generated by a docking algorithm having a RMSD value lower than the crystal structure resolution (R); (b) a novel consensus-based function defined as "protocol score"; and (c) the interaction energy maps (IEMs) analysis, based on the identification of key ligand-receptor interactions observed in the crystal structures.

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