BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge

Journal of Computer-aided Molecular Design
Emilio GallicchioRonald M Levy

Abstract

The binding energy distribution analysis method (BEDAM) protocol has been employed as part of the SAMPL4 blind challenge to predict the binding free energies of a set of octa-acid host-guest complexes. The resulting predictions were consistently judged as some of the most accurate predictions in this category of the SAMPL4 challenge in terms of quantitative accuracy and statistical correlation relative to the experimental values, which were not known at the time the predictions were made. The work has been conducted as part of a hands-on graduate class laboratory session. Collectively the students, aided by automated setup and analysis tools, performed the bulk of the calculations and the numerical and structural analysis. The success of the experiment confirms the reliability of the BEDAM methodology and it shows that physics-based atomistic binding free energy estimation models, when properly streamlined and automated, can be successfully employed by non-specialists.

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Citations

Aug 11, 2015·Journal of Molecular Recognition : JMR·Lauren WickstromRonald M Levy
May 28, 2015·Protein Science : a Publication of the Protein Society·Daniele Di MarinoEmilio Gallicchio
Apr 23, 2016·Computer Physics Communications·Emilio GallicchioRonald M Levy
Oct 26, 2016·Journal of Computer-aided Molecular Design·Nanjie DengRonald M Levy
Sep 30, 2016·Journal of Computer-aided Molecular Design·Juyong LeeBernard R Brooks
Feb 2, 2017·Beilstein Journal of Organic Chemistry·Sumudu P Leelananda, Steffen Lindert
Sep 19, 2018·Journal of Computer-aided Molecular Design·Yiğitcan EkenAngela K Wilson
Nov 13, 2018·Journal of Chemical Theory and Computation·Denise Kilburg, Emilio Gallicchio

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