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Dynamics of Water and Ions Near DNA: Comparison of Simulation to Time-Resolved Stokes-Shift Experiments

Journal of the American Chemical Society, 2009-02, Vol.131 (5), p.1724-1735

2009

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Molecular Dynamics–Markov State Model of Protein Ligand Binding and Allostery in CRIB-PDZ: Conformational Selection and Induced Fit

The journal of physical chemistry. B, 2017-06, Vol.121 (22), p.5509-5514

2017

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Allosteric Signaling in PDZ Energetic Networks: Embedding Error Analysis

The journal of physical chemistry. B, 2023-01, Vol.127 (3), p.623-633

2023

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Evolutionary Covariance Combined with Molecular Dynamics Predicts a Framework for Allostery in the MutS DNA Mismatch Repair Protein

The journal of physical chemistry. B, 2017-03, Vol.121 (9), p.2049-2061

2017

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Characterization of the Dynamics of an Essential Helix in the U1A Protein by Time-Resolved Fluorescence Measurements

The journal of physical chemistry. B, 2008-05, Vol.112 (19), p.6122-6130

2008

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Do Collective Atomic Fluctuations Account for Cooperative Effects? Molecular Dynamics Studies of the U1A−RNA Complex

Journal of the American Chemical Society, 2006-07, Vol.128 (28), p.8992-8993

2006

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Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction

Bioinformatics, 2006-04, Vol.22 (8), p.1007-1009

2006

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Investigation of domain structure in proteins via molecular dynamics simulation: application to HIV-1 protease dimer

Journal of the American Chemical Society, 1991-03, Vol.113 (7), p.2717-2721

1991

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Root Mean Square Deviation Probability Analysis of Molecular Dynamics Trajectories on DNA

Journal of chemical information and modeling, 2006-05, Vol.46 (3), p.1084-1093

2006

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Molecular Dynamics and Thermodynamics of Protein−RNA Interactions: Mutation of a Conserved Aromatic Residue Modifies Stacking Interactions and Structural Adaptation in the U1A−Stem Loop 2 RNA Complex

Journal of the American Chemical Society, 2001-03, Vol.123 (11), p.2548-2551

2001

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Molecular dynamics of B-DNA including water and counterions: a 140-ps trajectory for d(CGCGAATTCGCG) based on the GROMOS force field

Journal of the American Chemical Society, 1991-06, Vol.113 (13), p.5027-5040

1991

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Monte Carlo studies on the structure of a dilute aqueous solution of methane

Journal of the American Chemical Society, , Vol.100 (18), p.5705-5712

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Prediction of the protonation state of the active site aspartyl residues in HIV-1 protease-inhibitor complexes via molecular dynamics simulation

Journal of the American Chemical Society, 1993-05, Vol.115 (10), p.3883-3886

1993

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Theoretical evidence for water insertion in .alpha.-helix bending: molecular dynamics of Gly30 and Ala30 in vacuo and in solution

Journal of the American Chemical Society, 1991-07, Vol.113 (16), p.6145-6155

1991

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Theoretical studies of hydrogen bonding in liquid water and dilute aqueous solutions

The Journal of chemical physics, 1981-01, Vol.74 (1), p.622-632

1981

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Time dependence of nuclear Overhauser effects of duplex DNA from molecular dynamics trajectories

Journal of the American Chemical Society, 1991-06, Vol.113 (13), p.5041-5049

1991

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A theoretical study of polyelectrolyte effects in protein-DNA interactions: Monte Carlo free energy simulations on the ion atmosphere contribution to the thermodynamics of .lambda. repressor-operator complex formation

Journal of the American Chemical Society, 1991-07, Vol.113 (14), p.5211-5215

1991

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Mechanism for the destabilization of the dimer interface in a mutant HIV-1 protease: a molecular dynamics study

Journal of the American Chemical Society, 1993-02, Vol.115 (4), p.1231-1234

1993

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Conformational stability of dimethyl phosphate anion in water: liquid-state free energy simulations

Journal of the American Chemical Society, 1988-03, Vol.110 (6), p.1691-1694

1988

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Theoretical study of solvent effects on the conformational stability of acetylcholine

Journal of the American Chemical Society, 1974-06, Vol.96 (12), p.3769-3778

1974

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Aqueous hydration of benzene

Journal of the American Chemical Society, 1984-07, Vol.106 (15), p.4102-4108

1984

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A simple test for evaluating the truncation effects in simulations of systems involving charged groups

Chemical physics letters, 1995-03, Vol.234 (4), p.413-415

1995

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A theoretical study of the structure of liquid water based on quasi-component distribution functions

Journal of the American Chemical Society, 1977-12, Vol.99 (26), p.8392-8398

1977

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Monte Carlo computer simulation of hydrophobic bonding

Journal of the American Chemical Society, 1979-09, Vol.101 (19), p.5832-5833

1979

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A heuristic intermolecular potential function for formaldehyde-water based on ab initio molecular orbital calculations

Journal of the American Chemical Society, 1977-11, Vol.99 (24), p.7817-7822

1977

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Dynamics of Water and Ions Near DNA: Comparison of Simulation to Time-Resolved Stokes-Shift Experiments

Molecular Dynamics–Markov State Model of Protein Ligand Binding and Allostery in CRIB-PDZ: Conformational Selection and Induced Fit

Allosteric Signaling in PDZ Energetic Networks: Embedding Error Analysis

Evolutionary Covariance Combined with Molecular Dynamics Predicts a Framework for Allostery in the MutS DNA Mismatch Repair Protein

Characterization of the Dynamics of an Essential Helix in the U1A Protein by Time-Resolved Fluorescence Measurements

Do Collective Atomic Fluctuations Account for Cooperative Effects? Molecular Dynamics Studies of the U1A−RNA Complex

Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction

Investigation of domain structure in proteins via molecular dynamics simulation: application to HIV-1 protease dimer

Root Mean Square Deviation Probability Analysis of Molecular Dynamics Trajectories on DNA

Molecular Dynamics and Thermodynamics of Protein−RNA Interactions: Mutation of a Conserved Aromatic Residue Modifies Stacking Interactions and Structural Adaptation in the U1A−Stem Loop 2 RNA Complex

Molecular dynamics of B-DNA including water and counterions: a 140-ps trajectory for d(CGCGAATTCGCG) based on the GROMOS force field

Monte Carlo studies on the structure of a dilute aqueous solution of methane

Prediction of the protonation state of the active site aspartyl residues in HIV-1 protease-inhibitor complexes via molecular dynamics simulation

Theoretical evidence for water insertion in .alpha.-helix bending: molecular dynamics of Gly30 and Ala30 in vacuo and in solution

Theoretical studies of hydrogen bonding in liquid water and dilute aqueous solutions

Time dependence of nuclear Overhauser effects of duplex DNA from molecular dynamics trajectories

A theoretical study of polyelectrolyte effects in protein-DNA interactions: Monte Carlo free energy simulations on the ion atmosphere contribution to the thermodynamics of .lambda. repressor-operator complex formation

Mechanism for the destabilization of the dimer interface in a mutant HIV-1 protease: a molecular dynamics study

Conformational stability of dimethyl phosphate anion in water: liquid-state free energy simulations

Theoretical study of solvent effects on the conformational stability of acetylcholine

Aqueous hydration of benzene

A simple test for evaluating the truncation effects in simulations of systems involving charged groups

A theoretical study of the structure of liquid water based on quasi-component distribution functions

Monte Carlo computer simulation of hydrophobic bonding

A heuristic intermolecular potential function for formaldehyde-water based on ab initio molecular orbital calculations

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