(Q35572852)

8 August 2017

title

Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations (English)

1 reference

8 August 2017

3

Adrian E Roitberg

1 reference

8 August 2017

Yilin Meng

1

1 reference

8 August 2017

Danial Sabri Dashti

series ordinal

2

1 reference

8 August 2017

publication date

1 September 2011

1 reference

Journal of Chemical Theory and Computation

8 August 2017

published in

1 reference

8 August 2017

volume

7

1 reference

8 August 2017

issue

9

1 reference

8 August 2017

page(s)

2721-2727

1 reference

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

8 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics (FEP/REMD).

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Basic ingredients of free energy calculations: a review

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Statistically optimal analysis of samples from multiple equilibrium states

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Comparison of multiple Amber force fields and development of improved protein backbone parameters

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Replica exchange with solute tempering: a method for sampling biological systems in explicit water

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Electrostatic calculations of side-chain pK(a) values in myoglobin and comparison with NMR data for histidines

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Crystal structure of thioredoxin from Escherichia coli at 1.68 A resolution

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

The conserved, buried aspartic acid in oxidized Escherichia coli thioredoxin has a pKa of 7.5. Its titration produces a related shift in global stability

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Proton-transfer effects in the active-site region of Escherichia coli thioredoxin using two-dimensional 1H NMR.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Good practices in free-energy calculations

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Resolution exchange simulation.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Overcoming entropic barrier with coupled sampling at dual resolutions

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Improving the efficiency and reliability of free energy perturbation calculations using overlap sampling methods

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Effective Born radii in the generalized Born approximation: the importance of being perfect

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3223983

Calculation of the relative change in binding free energy of a protein-inhibitor complex

26 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22125475

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Increasing the Efficiency of Free Energy Calculations Using Parallel Tempering and Histogram Reweighting

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22125475

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT200153U

1 reference

release_2trsfz2kabgstgfc3peavwlfyq

8 August 2017

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/2trsfz2kabgstgfc3peavwlfyq

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMC publication ID

3223983

1 reference

8 August 2017

1 reference