(Q38253726)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21359274%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

title

Exploring the free-energy landscapes of biological systems with steered molecular dynamics (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21359274%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

1 reference

1

L Y Chen

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21359274%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

1 September 2017

language of work or name

English

0 references

publication date

25 February 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21359274%20AND%20SRC:MED&resulttype=core&format=json

Physical Chemistry Chemical Physics

23 January 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21359274%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

volume

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21359274%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

issue

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21359274%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

page(s)

6176-6183

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21359274%20AND%20SRC:MED&resulttype=core&format=json

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

23 January 2020

cites work

1 reference

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Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Forced unbinding of GPR17 ligands from wild type and R255I mutant receptor models through a computational approach

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Towards accurate free energy calculations in ligand protein-binding studies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Steered molecular dynamics simulations reveal the likelier dissociation pathway of imatinib from its targeting kinases c-Kit and Abl

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Computations of standard binding free energies with molecular dynamics simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Mechanism of selectivity in aquaporins and aquaglyceroporins.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Molecular modeling of hydration in drug design.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Calculation of protein-ligand binding affinities.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Comparison of free energy methods for molecular systems

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Scalable molecular dynamics with NAMD

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Calculating potentials of mean force from steered molecular dynamics simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Glycerol facilitator GlpF and the associated aquaporin family of channels

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

The glycerol facilitator GlpF its aquaporin family of channels, and their selectivity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

A model binding site for testing scoring functions in molecular docking

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Control of the selectivity of the aquaporin water channel family by global orientational tuning

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Water permeation across biological membranes: mechanism and dynamics of aquaporin-1 and GlpF.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Steered molecular dynamics investigations of protein function.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Free energy reconstruction from nonequilibrium single-molecule pulling experiments

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Cellular and molecular biology of the aquaporin water channels

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

VMD: visual molecular dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Hydration free energies of monovalent ions in transferable intermolecular potential four point fluctuating charge water: an assessment of simulation methodology and force field performance and transferability

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Determination of equilibrium free energy from nonequilibrium work measurements.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Free-energy landscape of glycerol permeation through aquaglyceroporin GlpF determined from steered molecular dynamics simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Dynamics and energetics of solute permeation through the Plasmodium falciparum aquaglyceroporin

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Binding of arachidonic acid and two flavonoid inhibitors to human 12- and 15-lipoxygenases: a steered molecular dynamics study.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Ligand unbinding from the estrogen receptor: a computational study of pathways and ligand specificity

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Assessment of nonequilibrium free energy methods

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Nonequilibrium fluctuation-dissipation theorem of Brownian dynamics

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Overcoming free energy barriers using unconstrained molecular dynamics simulations

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

Modeling protein-small molecule interactions: structure and thermodynamics of noble gases binding in a cavity in mutant phage T4 lysozyme L99A.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

The aquaporins, blueprints for cellular plumbing systems.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3111135

On the calculation of absolute free energies from molecular-dynamics or Monte Carlo data

31 August 2018

1 reference

https://api.crossref.org/works/10.1039%2FC0CP02799E

Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC0CP02799E

Climatic impact of tropical lowland deforestation on nearby montane cloud forests

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC0CP02799E

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC0CP02799E

Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21359274

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Protein-ligand binding affinity by nonequilibrium free energy methods

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21359274

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21359274

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1039/C0CP02799E

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21359274%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21359274%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

PubMed publication ID

21359274

1 reference