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Abbreviation : EDS
Long Form : enveloping distribution sampling
No. Year Title Co-occurring Abbreviation
2018 Accelerated Enveloping Distribution Sampling: Enabling Sampling of Multiple End States while Preserving Local Energy Minima. MD
2018 Comparison of free-energy methods using a tripeptide-water model system. BAR, TI
2016 Computational scheme for pH-dependent binding free energy calculation with explicit solvent. BAR, BZ, HREM, IPS, PME
2016 Replica exchange enveloping distribution sampling (RE-EDS): A robust method to estimate multiple free-energy differences from a single simulation. MD, RE-EDS, RE-EDS, TI
2015 Enhancing constant-pH simulation in explicit solvent with a two-dimensional replica exchange method. SGC
2014 Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange. HREX
2014 Integrated Hamiltonian sampling: a simple and versatile method for free energy simulations and conformational sampling. IHS, ITS
2013 Combination of Enveloping Distribution Sampling (EDS) of a Soft-Core Reference-State Hamiltonian with One-Step Perturbation to Predict the Effect of Side Chain Substitution on the Relative Stability of Right- and Left-Helical Folds of beta-Peptides. MD, OSP
2013 Efficient Combination of Environment Change and Alchemical Perturbation within the Enveloping Distribution Sampling (EDS) Scheme: Twin-System EDS and Application to the Determination of Octanol-Water Partition Coefficients. ---
10  2013 Enhanced conformational sampling using enveloping distribution sampling. ---
11  2013 Free Enthalpy Differences between alpha-, pi-, and 310-Helices of an Atomic Level Fine-Grained Alanine Deca-Peptide Solvated in Supramolecular Coarse-Grained Water. FG/CG
12  2012 Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution. ---
13  2012 Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett's Acceptance Ratio and Enveloping Distribution Sampling Methods. BAR, SGLD
14  2012 Free enthalpies of replacing water molecules in protein binding pockets. ---
15  2012 Using enveloping distribution sampling to compute the free enthalpy difference between right- and left-handed helices of a beta-peptide in solution. AD
16  2011 Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors. TI
17  2011 On the Use of Enveloping Distribution Sampling (EDS) to Compute Free Enthalpy Differences between Different Conformational States of Molecules: Application to 310-, alpha-, and pi-Helices. TI
18  2010 Ball-and-Stick Local Elevation Umbrella Sampling: Molecular Simulations Involving Enhanced Sampling within Conformational or Alchemical Subspaces of Low Internal Dimensionalities, Minimal Irrelevant Volumes, and Problem-Adapted Geometries. LE, US
19  2009 Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation. ---
20  2009 Simple, Efficient, and Reliable Computation of Multiple Free Energy Differences from a Single Simulation: A Reference Hamiltonian Parameter Update Scheme for Enveloping Distribution Sampling (EDS). ---
21  2008 Multiple free energies from a single simulation: extending enveloping distribution sampling to nonoverlapping phase-space distributions. ---