(Q30359360)

19 September 2017

Guidelines for the analysis of free energy calculations (English)

1 reference

19 September 2017

David L Mobley

3

0 references

author name string

Pavel V Klimovich

series ordinal

1

1 reference

PMC publication ID

4420631

19 September 2017

Michael R Shirts

series ordinal

2

1 reference

19 September 2017

26 March 2015

1 reference

Journal of Computer - Aided Molecular Design

19 September 2017

1 reference

19 September 2017

29

1 reference

19 September 2017

5

1 reference

19 September 2017

397-411

1 reference

https://scigraph.springernature.com/pub.10.1007/s10822-015-9840-9

19 September 2017

0 references

cites work

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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Linear basis function approach to efficient alchemical free energy calculations. 2. Inserting and deleting particles with coulombic interactions

3 June 2018

1 reference

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Converging free energies of binding in cucurbit[7]uril and octa-acid host-guest systems from SAMPL4 using expanded ensemble simulations

3 June 2018

1 reference

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Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

3 June 2018

1 reference

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GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

3 June 2018

1 reference

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Identifying low variance pathways for free energy calculations of molecular transformations in solution phase

3 June 2018

1 reference

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Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4420631

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

3 June 2018

1 reference

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Computations of standard binding free energies with molecular dynamics simulations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4420631

Statistically optimal analysis of samples from multiple equilibrium states

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4420631

Mechanical unfolding intermediates in titin modules.

3 June 2018

1 reference

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Free energy via molecular simulation: applications to chemical and biomolecular systems

3 June 2018

1 reference

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Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

3 June 2018

1 reference

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Matplotlib: A 2D Graphics Environment

21 January 2018

1 reference

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THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

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Variance minimization of free energy estimates from optimized expanded ensembles

21 January 2018

1 reference

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Good practices in free-energy calculations

21 January 2018

1 reference

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Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies

21 January 2018

1 reference

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Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

21 January 2018

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Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations.

21 January 2018

1 reference

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High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases

21 January 2018

1 reference

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Multistate Gaussian Model for Electrostatic Solvation Free Energies

21 January 2018

1 reference

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Electrostatic Potentials and Free Energies of Solvation of Polar and Charged Molecules

21 January 2018

1 reference

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Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

21 January 2018

1 reference

12 December 2020

In search of the hair-cell gating spring elastic properties of ankyrin and cadherin repeats

1 reference

12 December 2020

New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations

1 reference

12 December 2020

Linear-scaling soft-core scheme for alchemical free energy calculations

1 reference

12 December 2020

Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

1 reference

12 December 2020

Steered molecular dynamics simulations of force-induced protein domain unfolding

1 reference

12 December 2020

Small Molecule Solvation Free Energy: Enhanced Conformational Sampling Using Expanded Ensemble Molecular Dynamics Simulation

1 reference

12 December 2020

Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence

1 reference

12 December 2020

10.1007/S10822-015-9840-9

Identifiers

DOI

1 reference

journals/jcamd/KlimovichSM15

19 September 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

4420631

19 September 2017

PubMed publication ID

25808134

1 reference

PMC publication ID

4420631