Scalable molecular dynamics with NAMD (Q27860718)

5

0 references

Klaus Schulten

10

0 references

Elizabeth Villa

6

0 references

Rosemary Braun

2

0 references

James C Gumbart

4

object named as

James Gumbart

0 references

James C. Phillips

1

object named as

James C Phillips

0 references

author name string

Wei Wang

3

0 references

Christophe Chipot

7

0 references

Robert D Skeel

8

0 references

Laxmikant Kalé

Journal of Computational Chemistry

9

0 references

publication date

December 2005

0 references

published in

0 references

volume

26

0 references

page(s)

1781-802

0 references

issue

16

0 references

cites work

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Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map

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Calculating potentials of mean force from steered molecular dynamics simulations

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Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase

29 September 2017

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29 September 2017

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Electrostatic Tuning of Permeation and Selectivity in Aquaporin Water Channels

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Gating of MscL Studied by Steered Molecular Dynamics

29 September 2017

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Mechanisms of selectivity in channels and enzymes studied with interactive molecular dynamics

29 September 2017

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Forced detachment of the CD2-CD58 complex

29 September 2017

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Fluorescence resonance energy transfer over approximately 130 basepairs in hyperstable lac repressor-DNA loops

29 September 2017

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Steered molecular dynamics studies of titin I1 domain unfolding

29 September 2017

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Pressure-induced water transport in membrane channels studied by molecular dynamics

29 September 2017

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The mechanism of glycerol conduction in aquaglyceroporins.

29 September 2017

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Steered molecular dynamics investigations of protein function.

29 September 2017

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From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

29 September 2017

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Steered molecular dynamics and mechanical functions of proteins

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The key event in force-induced unfolding of Titin's immunoglobulin domains

29 September 2017

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Steered molecular dynamics simulation of the Rieske subunit motion in the cytochrome bc(1) complex

29 September 2017

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Unbinding of retinoic acid from its receptor studied by steered molecular dynamics

29 September 2017

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Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations

29 September 2017

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Binding of the estrogen receptor to DNA. The role of waters

29 September 2017

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Molecular dynamics study of unbinding of the avidin-biotin complex

29 September 2017

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Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force

29 September 2017

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Components of ubiquitin-protein ligase system. Resolution, affinity purification, and role in protein breakdown

29 September 2017

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Treatment of electrostatic effects in macromolecular modeling

29 September 2017

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Multiple grid methods for classical molecular dynamics.

29 September 2017

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The effects of truncating long-range forces on protein dynamics.

2 June 2018

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Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A.

2 June 2018

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Collective Diffusion Model for Water Permeation through Microscopic Channels

27 November 2018

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Structural insights into how the MIDAS ion stabilizes integrin binding to an RGD peptide under force

27 November 2018

1 reference

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Modelling DNA loops using continuum and statistical mechanics.

27 November 2018

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Overcoming free energy barriers using unconstrained molecular dynamics simulations

27 November 2018

1 reference

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Langevin dynamics in constant pressure extended systems.

27 November 2018

1 reference

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Force-clamp spectroscopy monitors the folding trajectory of a single protein.

27 November 2018

1 reference

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Structural basis for cooperative DNA binding by CAP and lac repressor.

27 November 2018

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The mechanical stability of ubiquitin is linkage dependent

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2486339

Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2486339

Molecular dynamics study of aquaporin-1 water channel in a lipid bilayer.

27 November 2018

1 reference

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Constant-pressure equations of motion.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2486339

The effect of point mutations on the free energy of transmembrane alpha-helix dimerization.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2486339

Steered molecular dynamics simulations of force-induced protein domain unfolding

27 November 2018

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12 December 2020

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

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12 December 2020

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

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12 December 2020

Hidden thermodynamics of mutant proteins: a molecular dynamics analysis

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12 December 2020

MDScope — a visual computing environment for structural biology

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COCI

https://opencitations.net/index/coci/api/v1/citations/10.1016/0010-4655(95)00045-H

22 October 2022

Identifiers

DOI

10.1002/JCC.20289

1 reference

journals/jcc/PhillipsBWGTVCSKS05

151601

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

151601

1 reference

1 reference

1 reference