Replica-Exchange Enveloping Distribution Sampling: Calculation of Relative Free Energies in GROMOS
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Date
2022-04-27
Publication Type
Journal Article
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Abstract
Free-energy calculations based on molecular dynamics (MD) simulations are playing an increasingly important role for computer-aided drug design and material discovery in recent years. Free-energy differences between pairs of end-states can be estimated using well-established methods such as thermodynamic integration (TI) or Bennett’s acceptance ratio (BAR). An attractive alternative is the recently developed replica-exchange enveloping distribution sampling (RE-EDS) method, which enables estimating relative free-energy differences between multiple molecules from a single simulation. Here, we provide an introduction to the principles underlying RE-EDS and give an overview of the RE-EDS pipeline. In addition, we provide a description of the two complementary tools RestraintMaker and amber2gromos. We briefly discuss the findings of three recent applications of RE-EDS to calculate relative binding or hydration free energies. In all three studies, good agreement was found between the results obtained using RE-EDS and experimental values as well as values obtained using other free-energy methods.
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published
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Journal / series
Volume
76 (4)
Pages / Article No.
327 - 330
Publisher
Swiss Chemical Society
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Methods
Software
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Date created
Subject
Computational chemistry; Free energy; RE-EDS
Organisational unit
09458 - Riniker, Sereina Z. / Riniker, Sereina Z.
08820 - Hünenberger, Philippe (Tit.-Prof.)
Notes
Funding
178762 - Passive Membrane-Permeability Prediction for Peptides and Peptidomimetics Using Computational Methods (SNF)
175944 - A Combinatorial Computational Chemistry Approach to Force-Field Development (SNF)
175944 - A Combinatorial Computational Chemistry Approach to Force-Field Development (SNF)