Abstract
The critical issues in docking include the prediction of the correct binding pose and the accurate estimation of the corresponding binding affinity. Different docking methodologies have all been successful in reproducing the crystallographic binding modes, but struggle when predicting the corresponding binding affinities. The rescoring of docking poses using the MM-GB/SA technique has emerged as an important computational approach in structure-based lead optimization as it provides for congeneric molecules, clearly superior correlations with experimental data to those obtained with typical docking scoring functions. Although the technique has been collectively referred as MM-GB/SA, there are in fact many flavors in the literature. Here we describe the details of our MM-GB/SA scoring protocol, highlighting not only its strengths but also the limitations.
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Acknowledgment
The author would like to thank Alan Mathiowetz from Pfizer and Mario Cardozo from Amgen who greatly contributed to the development of the MM-GB/SA protocol described in this work.
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Guimarães, C.R.W. (2012). MM-GB/SA Rescoring of Docking Poses. In: Baron, R. (eds) Computational Drug Discovery and Design. Methods in Molecular Biology, vol 819. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-465-0_17
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DOI: https://doi.org/10.1007/978-1-61779-465-0_17
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