Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering (Q37701321)

22 August 2017

Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering (English)

1 reference

22 August 2017

1

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2 June 2020

Julian Tirado-Rives

series ordinal

2

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2 June 2020

author name string

William L Jorgensen

series ordinal

3

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2 June 2020

publication date

17 January 2014

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Journal of Chemical Theory and Computation

22 August 2017

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2 June 2020

volume

10

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2 June 2020

issue

2

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2 June 2020

page(s)

565-571

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Optimization of benzyloxazoles as non-nucleoside inhibitors of HIV-1 reverse transcriptase to enhance Y181C potency

2 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Computationally-guided optimization of a docking hit to yield catechol diethers as potent anti-HIV agents

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Efficient discovery of potent anti-HIV agents targeting the Tyr181Cys variant of HIV reverse transcriptase

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2).

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Equilibrium sampling in biomolecular simulations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Eastern extension of azoles as non-nucleoside inhibitors of HIV-1 reverse transcriptase; cyano group alternatives

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Prediction of the water content in protein binding sites

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Efficient drug lead discovery and optimization

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Optimization of azoles as anti-human immunodeficiency virus agents guided by free-energy calculations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Molecular simulation methods in drug discovery: a prospective outlook

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Efficient conformational sampling of peptides adsorbed onto inorganic surfaces: insights from a quartz binding peptide

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

On easy implementation of a variant of the replica exchange with solute tempering in GROMACS.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Hamiltonian replica exchange molecular dynamics using soft-core interactions

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Optimization of diarylamines as non-nucleoside inhibitors of HIV-1 reverse transcriptase

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Roles of Conformational and Positional Adaptability in Structure-Based Design of TMC125-R165335 (Etravirine) and Related Non-nucleoside Reverse Transcriptase Inhibitors That Are Highly Potent and Effective against Wild-Type and Drug-Resistant HIV-1 V

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3985685

Conformation of alkanes in the gas phase and pure liquids

3 December 2018

1 reference

12 December 2020

Optimization of pyrimidinyl- and triazinyl-amines as non-nucleoside inhibitors of HIV-1 reverse transcriptase

1 reference

12 December 2020

Computer-aided design of non-nucleoside inhibitors of HIV-1 reverse transcriptase

1 reference

12 December 2020

Improved Replica Exchange Method for Native-State Protein Sampling

1 reference

12 December 2020

Reversible temperature and pressure denaturation of a protein fragment: a replica exchange molecular dynamics simulation study

1 reference

12 December 2020

Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT400989X

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24803853%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

1 reference

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2 June 2020

PubMed publication ID

24803853

1 reference