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Molecular Dynamics and Protein Function

Proceedings of the National Academy of Sciences - PNAS, 2005-05, Vol.102 (19), p.6679-6685

2005

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CHARMM: The biomolecular simulation program

Journal of computational chemistry, 2009-07, Vol.30 (10), p.1545-1614

2009

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Injection of Tibetan crust beneath the south Qaidam Basin: Evidence from INDEPTH IV wide-angle seismic data

Journal of Geophysical Research, 2011-07, Vol.116 (B7), p.n/a, Article B07301

2011

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Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA

Nature (London), 2005-03, Vol.434 (7033), p.612-618

2005

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Allosteric communication in myosin V: from small conformational changes to large directed movements

PLoS computational biology, 2008-08, Vol.4 (8), p.e1000129-e1000129

2008

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Active‐Source Seismic Tomography at the Brady Geothermal Field, Nevada, with Dense Nodal and Fiber‐Optic Seismic Arrays

Seismological research letters, 2018-09, Vol.89 (5), p.1629-1640

2018

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Laboratory Tests of Three Z‐Land Fairfield Nodal 5‐Hz, Three‐Component Sensors

Seismological research letters, 2018-09, Vol.89 (5), p.1601-1608

2018

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All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

The journal of physical chemistry. B, 1998-04, Vol.102 (18), p.3586-3616

1998

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Ambient-noise tomography of north Tibet limits geological terrane signature to upper-middle crust

Geophysical research letters, 2013-03, Vol.40 (5), p.808-813

2013

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Molecular Properties from Combined QM/MM Methods. 2. Chemical Shifts in Large Molecules

The journal of physical chemistry. B, 2000-04, Vol.104 (15), p.3721-3743

2000

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Calculation of Free-Energy Differences by Confinement Simulations. Application to Peptide Conformers

The journal of physical chemistry. B, 2009-07, Vol.113 (29), p.9728-9740

2009

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Triosephosphate Isomerase: A Theoretical Comparison of Alternative Pathways

Journal of the American Chemical Society, 2001-03, Vol.123 (10), p.2284-2290

2001

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A Conformational Transition in the Myosin VI Converter Contributes to the Variable Step Size

Biophysical journal, 2011-11, Vol.101 (10), p.2436-2444

2011

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Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility

Journal of molecular biology, 2002-01, Vol.315 (1), p.21-52

2002

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The Missing Link between Thermodynamics and Structure in F1-ATPase

Proceedings of the National Academy of Sciences - PNAS, 2003-02, Vol.100 (3), p.874-879

2003

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Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin

Protein science, 1998-03, Vol.7 (3), p.649-666

1998

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Association between the Tumor Necrosis Factor Locus and the Clinical Outcome of Leishmania chagasi Infection

Infection and Immunity, 2002-12, Vol.70 (12), p.6919-6925

2002

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A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

Nature, 2007-12, Vol.450 (7171), p.913-916

2007

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Large Amplitude Conformational Change in Proteins Explored with a Plastic Network Model: Adenylate Kinase

Journal of molecular biology, 2005-09, Vol.352 (4), p.807-822

2005

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Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin

Journal of the American Chemical Society, 1990-12, Vol.112 (25), p.9161-9175

1990

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Protein folding dynamics: The diffusion‐collision model and experimental data

Protein science, 1994-04, Vol.3 (4), p.650-668

1994

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Molecular Dynamics Simulations of Biomolecules

Accounts of chemical research, 2002-06, Vol.35 (6), p.321-323

Karplus, Martin

2002

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Early postnatal dexamethasone treatment and increased incidence of cerebral palsy

Archives of disease in childhood. Fetal and neonatal edition, 2000-11, Vol.83 (3), p.F177-F181

2000

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Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

Journal of computer-aided molecular design, 2003-12, Vol.17 (12), p.861-880

2003

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Increasing Normal Modes Analysis Accuracy: The SPASIBA Spectroscopic Force Field Introduced into the CHARMM Program

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2004-05, Vol.108 (18), p.4019-4029

2004

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Molecular Dynamics and Protein Function

CHARMM: The biomolecular simulation program

Injection of Tibetan crust beneath the south Qaidam Basin: Evidence from INDEPTH IV wide-angle seismic data

Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA

Allosteric communication in myosin V: from small conformational changes to large directed movements

Active‐Source Seismic Tomography at the Brady Geothermal Field, Nevada, with Dense Nodal and Fiber‐Optic Seismic Arrays

Laboratory Tests of Three Z‐Land Fairfield Nodal 5‐Hz, Three‐Component Sensors

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

Ambient-noise tomography of north Tibet limits geological terrane signature to upper-middle crust

Molecular Properties from Combined QM/MM Methods. 2. Chemical Shifts in Large Molecules

Calculation of Free-Energy Differences by Confinement Simulations. Application to Peptide Conformers

Triosephosphate Isomerase: A Theoretical Comparison of Alternative Pathways

A Conformational Transition in the Myosin VI Converter Contributes to the Variable Step Size

Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility

The Missing Link between Thermodynamics and Structure in F1-ATPase

Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin

Association between the Tumor Necrosis Factor Locus and the Clinical Outcome of Leishmania chagasi Infection

A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

Large Amplitude Conformational Change in Proteins Explored with a Plastic Network Model: Adenylate Kinase

Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin

Protein folding dynamics: The diffusion‐collision model and experimental data

Molecular Dynamics Simulations of Biomolecules

Early postnatal dexamethasone treatment and increased incidence of cerebral palsy

Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

Increasing Normal Modes Analysis Accuracy: The SPASIBA Spectroscopic Force Field Introduced into the CHARMM Program

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