Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett’s Acceptance Ratio and Enveloping Distribution Sampling Methods (Q56989498)

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scientific article published on 03 July 2012

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English	Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett’s Acceptance Ratio and Enveloping Distribution Sampling Methods	scientific article published on 03 July 2012

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scholarly article

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1 March 2020

Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett's Acceptance Ratio and Enveloping Distribution Sampling Methods (English)

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1 March 2020

1

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1 March 2020

Benjamin L. Miller

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1 March 2020

author name string

Xiongwu Wu

4

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1 March 2020

Bernard R Brooks

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publication date

3 July 2012

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Journal of Chemical Theory and Computation

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10

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3650-3662

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1 March 2020

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

1 reference

https://pubmed.ncbi.nlm.nih.gov/26593010

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Free energies of ligand binding for structurally diverse compounds

1 reference

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Alchemical free energy calculations and multiple conformational substates

1 reference

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Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration

1 reference

https://pubmed.ncbi.nlm.nih.gov/26593010

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Enveloping distribution sampling: a method to calculate free energy differences from a single simulation

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Predicting absolute ligand binding free energies to a simple model site

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Are current molecular dynamics force fields too helical?

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Multiple free energies from a single simulation: extending enveloping distribution sampling to nonoverlapping phase-space distributions.

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Backbone relaxation coupled to the ionization of internal groups in proteins: a self-guided Langevin dynamics study

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Open science grid study of the coupling between conformation and water content in the interior of a protein

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Statistically optimal analysis of samples from multiple equilibrium states

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Unorthodox uses of Bennett's acceptance ratio method

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Self-guided Langevin dynamics study of regulatory interactions in NtrC.

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CHARMM: the biomolecular simulation program

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Comparison of three enveloping distribution sampling Hamiltonians for the estimation of multiple free energy differences from a single simulation.

1 reference

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Hydration free energies of amino acids: why side chain analog data are not enough

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Limits of Free Energy Computation for Protein-Ligand Interactions

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Principles of stop-codon reading on the ribosome

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Characterizing the denatured state of human prion 121-230

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Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations

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Alchemical free energy methods for drug discovery: progress and challenges

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Non-Boltzmann sampling and Bennett's acceptance ratio method: how to profit from bending the rules.

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Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method.

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Toward canonical ensemble distribution from self-guided Langevin dynamics simulation

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MSCALE: A General Utility for Multiscale Modeling.

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Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors.

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Let's get honest about sampling.

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Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensemble

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Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations

1 reference

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12 December 2020

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Alchemical prediction of hydration free energies for SAMPL.

1 reference

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Thermodynamic integration to predict host-guest binding affinities

1 reference

https://pubmed.ncbi.nlm.nih.gov/26593010

12 December 2020

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Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM).

1 reference

https://pubmed.ncbi.nlm.nih.gov/26593010

12 December 2020

based on heuristic

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Blind prediction of host-guest binding affinities: a new SAMPL3 challenge.

1 reference

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12 December 2020

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

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A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods

1 reference

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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).

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Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange.

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QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling: Application to an Enzymatic Reaction

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VMD: visual molecular dynamics

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Identifiers

10.1021/CT300116R

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Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26593010%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26593010%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

1 reference

Europe PubMed Central

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26593010%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

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