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J Chem Inf Model. 2013 Jan 28;53(1):159-75. doi: 10.1021/ci300326d. Epub 2013 Jan 9.

An automated docking protocol for hERG channel blockers.

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  • 1Department of Pharmacy and Biotechnology, Alma Mater Studiorum, Universit√† di Bologna, Via Belmeloro 6, 40126 Bologna, Italy.


A docking protocol aimed at obtaining a consistent qualitative and quantitative picture of binding for a series of hERG channel blockers is presented. To overcome the limitations experienced by standard procedures when docking blockers at hERG binding site, we designed a strategy that explicitly takes into account the conformations of the channel, their possible intrinsic symmetry, and the role played by the configurational entropy of ligands. The protocol was developed on a series of congeneric sertindole derivatives, allowing us to satisfactorily explain the structure-activity relationships for this set of blockers. In addition, we show that the performance of structure-based models relying on multiple-receptor conformations statistically increases when the protein conformations are chosen in such a way as to capture relevant structural features at the binding site. The protocol was then successfully applied to a series of structurally unrelated blockers.

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