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

Content Provider	Springer Nature Link
Author	Gallicchio, Emilio Chen, Haoyuan Chen, He Fitzgerald, Michael Gao, Yang He, Peng Kalyanikar, Malathi Kao, Chuan Lu, Beidi Niu, Yijie Pethe, Manasi Zhu, Jie Levy, Ronald M.
Copyright Year	2015
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.
Starting Page	315
Ending Page	325
Page Count	11
File Format	PDF
ISSN	0920654X
Journal	Journal of Computer-Aided Molecular Design
Volume Number	29
Issue Number	4
e-ISSN	15734951
Language	English
Publisher	Springer International Publishing
Publisher Date	2015-03-01
Publisher Place	Cham
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Binding energy distribution analysis method Implicit solvation Analytic generalized Born plus non-polar model Blind prediction Physical Chemistry Computer Applications in Chemistry Animal Anatomy / Morphology / Histology
Content Type	Text
Resource Type	Article
Subject	Drug Discovery Physical and Theoretical Chemistry Computer Science Applications

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