Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials

Sergio A. Hassan; Ernest L. Mehler; Daqun Zhang; Harel Weinstein

doi:10.1002/prot.10330

Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.10330 ◽

2003 ◽

Vol 51 (1) ◽

pp. 109-125 ◽

Cited By ~ 49

Author(s):

Sergio A. Hassan ◽

Ernest L. Mehler ◽

Daqun Zhang ◽

Harel Weinstein

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Electrostatic Model ◽

Model Based ◽

Screened Coulomb Potentials ◽

Dynamics Simulations ◽

Coulomb Potentials

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Calibration of Nanocrystal Grain Boundary Model Based on Polycrystal Plasticity Using Molecular Dynamics Simulations

International Journal for Multiscale Computational Engineering ◽

10.1615/intjmultcompeng.v8.i5.60 ◽

2010 ◽

Vol 8 (5) ◽

pp. 509-522 ◽

Cited By ~ 4

Author(s):

Sangmin Lee ◽

Veera Sundararaghavan

Keyword(s):

Molecular Dynamics ◽

Grain Boundary ◽

Molecular Dynamics Simulations ◽

Model Based ◽

Polycrystal Plasticity ◽

Boundary Model ◽

Dynamics Simulations

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Pharmacophore model-based virtual screening, docking, biological evaluation and molecular dynamics simulations for inhibitors discovery against α-tryptophan synthase from Mycobacterium tuberculosis

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2020.1715259 ◽

2020 ◽

pp. 1-11 ◽

Cited By ~ 3

Author(s):

Sadia Naz ◽

Umar Farooq ◽

Sara Khan ◽

Rizwana Sarwar ◽

Yahia Nasser Mabkhot ◽

...

Keyword(s):

Molecular Dynamics ◽

Mycobacterium Tuberculosis ◽

Virtual Screening ◽

Molecular Dynamics Simulations ◽

Pharmacophore Model ◽

Biological Evaluation ◽

Tryptophan Synthase ◽

Model Based ◽

Dynamics Simulations

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Erratum: “A pure H2O isolated line-shape model based on classical molecular dynamics simulations of velocity changes and semi-classical calculations of speed-dependent collisional parameters” [J. Chem. Phys. 136, 154310 (2012)]

The Journal of Chemical Physics ◽

10.1063/1.4719804 ◽

2012 ◽

Vol 136 (18) ◽

pp. 189901 ◽

Cited By ~ 3

Author(s):

N. H. Ngo ◽

H. Tran ◽

R. R. Gamache

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Line Shape ◽

Chem Phys ◽

Shape Model ◽

Model Based ◽

Classical Molecular Dynamics ◽

Velocity Changes ◽

Dynamics Simulations

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An isolated line-shape model based on the Keilson–Storer function for velocity changes. II. Molecular dynamics simulations and the Q(1) lines for pure H2

The Journal of Chemical Physics ◽

10.1063/1.3247898 ◽

2009 ◽

Vol 131 (15) ◽

pp. 154303 ◽

Cited By ~ 37

Author(s):

H. Tran ◽

J.-M. Hartmann ◽

F. Chaussard ◽

M. Gupta

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Line Shape ◽

Shape Model ◽

Model Based ◽

Velocity Changes ◽

Dynamics Simulations

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A pure H2O isolated line-shape model based on classical molecular dynamics simulations of velocity changes and semi-classical calculations of speed-dependent collisional parameters

The Journal of Chemical Physics ◽

10.1063/1.4704675 ◽

2012 ◽

Vol 136 (15) ◽

pp. 154310 ◽

Cited By ~ 28

Author(s):

N. H. Ngo ◽

H. Tran ◽

R. R. Gamache

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Line Shape ◽

Shape Model ◽

Model Based ◽

Classical Molecular Dynamics ◽

Velocity Changes ◽

Dynamics Simulations

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The DNA-esperamicin A1 complex. A model based on solvated molecular dynamics simulations

Journal of the American Chemical Society ◽

10.1021/ja00080a003 ◽

1994 ◽

Vol 116 (1) ◽

pp. 15-29 ◽

Cited By ~ 22

Author(s):

D. R. Langley ◽

J. Golik ◽

B. Krishman ◽

T. W. Doyle ◽

D. L. Beveridge

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Model Based ◽

Dynamics Simulations

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A Large Strain Isotropic Elasticity Model Based on Molecular Dynamics Simulations of a Metallic Glass

Journal of Elasticity ◽

10.1007/s10659-010-9297-y ◽

2011 ◽

Vol 104 (1-2) ◽

pp. 281-302 ◽

Cited By ~ 7

Author(s):

David L. Henann ◽

Lallit Anand

Keyword(s):

Molecular Dynamics ◽

Metallic Glass ◽

Molecular Dynamics Simulations ◽

Large Strain ◽

Model Based ◽

Isotropic Elasticity ◽

Dynamics Simulations

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CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model

Journal of Computational Chemistry ◽

10.1002/jcc.20077 ◽

2004 ◽

Vol 25 (12) ◽

pp. 1504-1514 ◽

Cited By ~ 308

Author(s):

Sandeep Patel ◽

Alexander D. Mackerell ◽

Charles L. Brooks

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Electrostatic Model ◽

Dynamics Simulations ◽

Fluctuating Charge Force Field ◽

Solvent Properties

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Dependence of DNA Polymerase Replication Rate on External Forces: A Model Based on Molecular Dynamics Simulations

Biophysical Journal ◽

10.1529/biophysj.103.039313 ◽

2004 ◽

Vol 87 (3) ◽

pp. 1478-1497 ◽

Cited By ~ 24

Author(s):

Ioan Andricioaei ◽

Anita Goel ◽

Dudley Herschbach ◽

Martin Karplus

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Dna Polymerase ◽

Replication Rate ◽

Model Based ◽

Dynamics Simulations ◽

External Forces

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Molecular Dynamics Simulations of a Protein-Protein Dimer: Particle-Mesh Ewald Electrostatic Model Yields Far Superior Results to Standard Cutoff Model

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.1999.10508328 ◽

1999 ◽

Vol 16 (6) ◽

pp. 1205-1218 ◽

Cited By ~ 52

Author(s):

Osmar Norberto de Souza ◽

Rick L. Ornstein

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Electrostatic Model ◽

Particle Mesh Ewald ◽

Protein Dimer ◽

Dynamics Simulations

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