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Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning

PLoS computational biology, 2019-04, Vol.15 (4), p.e1006954

2019

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Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin

The journal of physical chemistry. B, 2012-07, Vol.116 (29), p.8584-8603

2012

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Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI

The Journal of chemical physics, 2011-02, Vol.134 (8), p.085103-085103-25

2011

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Development of Multiscale Models for Complex Chemical Systems: From H+H 2 to Biomolecules (Nobel Lecture)

Angewandte Chemie International Edition, 2014-09, Vol.53 (38), p.9992-10005

Karplus, Martin

2014

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On the calculation of entropy from covariance matrices of the atomic fluctuations

The Journal of chemical physics, 2001-10, Vol.115 (14), p.6289-6292

2001

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Aspects of Protein Reaction Dynamics: Deviations from Simple Behavior

The journal of physical chemistry. B, 2000-01, Vol.104 (1), p.11-27

Karplus, Martin

2000

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Significance of Molecular Dynamics Simulations for Life Sciences

Israel journal of chemistry, 2014-08, Vol.54 (8-9), p.1042-1051

2014

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Intrinsic motions along an enzymatic reaction trajectory

Nature, 2007-12, Vol.450 (7171), p.838-844

2007

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Free Energy Simulations Come of Age: Protein−Ligand Recognition

Accounts of chemical research, 2002-06, Vol.35 (6), p.430-437

2002

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Free energy disconnectivity graphs: Application to peptide models

The Journal of chemical physics, 2002-12, Vol.117 (23), p.10894-10903

2002

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Free Energy Simulations of Receptor-Binding Domain Opening of the SARS-CoV‑2 Spike Indicate a Barrierless Transition with Slow Conformational Motions

The journal of physical chemistry. B, 2023-10, Vol.127 (40), p.8565-8575

2023

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The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics

The Journal of chemical physics, 1997-01, Vol.106 (4), p.1495-1517

1997

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Is a “Proton Wire” Concerted or Stepwise? A Model Study of Proton Transfer in Carbonic Anhydrase

The journal of physical chemistry. B, 2003-01, Vol.107 (4), p.1071-1078

2003

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A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method

The journal of physical chemistry. B, 2001-01, Vol.105 (2), p.569-585

2001

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A Smooth Solvation Potential Based on the Conductor-Like Screening Model

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 1999-12, Vol.103 (50), p.11060-11079

1999

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Quantum Mechanics/Molecular Mechanics Studies of Triosephosphate Isomerase-Catalyzed Reactions: Effect of Geometry and Tunneling on Proton-Transfer Rate Constants

Journal of the American Chemical Society, 2002-03, Vol.124 (12), p.3093-3124

2002

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Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2000-03, Vol.104 (8), p.1720-1735

2000

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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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Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise

The Journal of chemical physics, 2008-07, Vol.129 (2), p.024102-024102

2008

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The distance fluctuation criterion for melting: Comparison of square-well and Morse potential models for clusters and homopolymers

The Journal of chemical physics, 2002-02, Vol.116 (5), p.2323-2329

2002

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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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Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations

The Journal of chemical physics, 2000-01, Vol.112 (3), p.1133-1149

2000

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Dynamic Distance Disorder in Proteins Is Caused by Trapping

The journal of physical chemistry. B, 2006-05, Vol.110 (19), p.9363-9367

2006

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Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method

The Journal of chemical physics, 2005-03, Vol.122 (11), p.114903-114903

2005

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Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence

The Journal of chemical physics, 2004-02, Vol.120 (6), p.2618-2628

2004

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Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learning

Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin

Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI

Development of Multiscale Models for Complex Chemical Systems: From H+H 2 to Biomolecules (Nobel Lecture)

On the calculation of entropy from covariance matrices of the atomic fluctuations

Aspects of Protein Reaction Dynamics: Deviations from Simple Behavior

Significance of Molecular Dynamics Simulations for Life Sciences

Intrinsic motions along an enzymatic reaction trajectory

Free Energy Simulations Come of Age: Protein−Ligand Recognition

Free energy disconnectivity graphs: Application to peptide models

Free Energy Simulations of Receptor-Binding Domain Opening of the SARS-CoV‑2 Spike Indicate a Barrierless Transition with Slow Conformational Motions

The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics

Is a “Proton Wire” Concerted or Stepwise? A Model Study of Proton Transfer in Carbonic Anhydrase

A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method

A Smooth Solvation Potential Based on the Conductor-Like Screening Model

Quantum Mechanics/Molecular Mechanics Studies of Triosephosphate Isomerase-Catalyzed Reactions: Effect of Geometry and Tunneling on Proton-Transfer Rate Constants

Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches

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

Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise

The distance fluctuation criterion for melting: Comparison of square-well and Morse potential models for clusters and homopolymers

Triosephosphate Isomerase: A Theoretical Comparison of Alternative Pathways

Molecular properties from combined QM/MM methods. I. Analytical second derivative and vibrational calculations

Dynamic Distance Disorder in Proteins Is Caused by Trapping

Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method

Free energy simulations: use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence

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