Free energy perturbation method for chemical reactions in the condensed phase: a dynamic approach based on a combined quantum and molecular mechanics potential

Paul A. Bash; Martin J. Field; Martin Karplus

doi:10.1021/ja00260a028

Free energy perturbation method for chemical reactions in the condensed phase: a dynamic approach based on a combined quantum and molecular mechanics potential

Journal of the American Chemical Society ◽

10.1021/ja00260a028 ◽

1987 ◽

Vol 109 (26) ◽

pp. 8092-8094 ◽

Cited By ~ 219

Author(s):

Paul A. Bash ◽

Martin J. Field ◽

Martin Karplus

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Molecular Mechanics ◽

Chemical Reactions ◽

Condensed Phase ◽

Free Energy Perturbation ◽

Dynamic Approach ◽

Energy Perturbation

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A quantum molecular dynamic free energy perturbation method applied to chemical reactions in the condensed phase

Journal of Molecular Graphics ◽

10.1016/s0263-7855(98)80029-5 ◽

1988 ◽

Vol 6 (4) ◽

pp. 219

Author(s):

PaulA. Bash ◽

MartinJ. Field ◽

Martin Karplus

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Molecular Dynamic ◽

Chemical Reactions ◽

Condensed Phase ◽

Free Energy Perturbation ◽

Quantum Molecular Dynamic ◽

Energy Perturbation

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Characterization of the effect of functional groups substitution at the 2-position of adenine on the stability of a duplex dodecamer d(CGCGAATTCGCG)2 by molecular mechanics and free energy perturbation method

Computer Simulation of Biomolecular Systems ◽

10.1007/978-94-017-1120-3_20 ◽

1997 ◽

pp. 563-600

Author(s):

Hiroshi Kuramochi ◽

U. Chandra Singh

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Molecular Mechanics ◽

Functional Groups ◽

Free Energy Perturbation ◽

Energy Perturbation ◽

The Stability

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A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): Application to highly solvent-dependent reactions

Journal of Computational Chemistry ◽

10.1002/jcc.21653 ◽

2010 ◽

Vol 32 (5) ◽

pp. 778-786 ◽

Cited By ~ 12

Author(s):

Kenji Hori ◽

Toru Yamaguchi ◽

Keita Uezu ◽

Michinori Sumimoto

Keyword(s):

Monte Carlo ◽

Free Energy ◽

Monte Carlo Simulations ◽

Perturbation Method ◽

Free Energy Perturbation ◽

Quantum Mechanical ◽

Quantum Mechanical Calculations ◽

Energy Perturbation

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Binding free energy calculation of human beta defensin 3 with negatively charged lipid bilayer using free energy perturbation method

Biophysical Chemistry ◽

10.1016/j.bpc.2021.106662 ◽

2021 ◽

pp. 106662

Author(s):

Ann Brewer ◽

Liqun Zhang

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Lipid Bilayer ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Free Energy Perturbation ◽

Energy Calculation ◽

Binding Free Energy Calculation ◽

Energy Perturbation

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Ab initio quantum mechanics-based free energy perturbation method for calculating relative solvation free energies

Journal of Computational Chemistry ◽

10.1002/jcc.20510 ◽

2006 ◽

Vol 28 (2) ◽

pp. 491-494 ◽

Cited By ~ 24

Author(s):

M. Rami Reddy ◽

U. C. Singh ◽

Mark D. Erion

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Perturbation Method ◽

Ab Initio ◽

Free Energy Perturbation ◽

Free Energies ◽

Energy Perturbation ◽

Solvation Free Energies

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Molecular recognition by β-cyclodextrin derivatives: molecular dynamics, free-energy perturbation and molecular mechanics/ Poisson-Boltzmann surface area goals and problems

Theoretical Chemistry Accounts ◽

10.1007/s00214-002-0384-4 ◽

2002 ◽

Vol 108 (5) ◽

pp. 286-292 ◽

Cited By ~ 14

Author(s):

Ivan Beà ◽

Carlos Jaime ◽

Peter Kollman

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Recognition ◽

Molecular Mechanics ◽

Surface Area ◽

Free Energy Perturbation ◽

Cyclodextrin Derivatives ◽

Poisson Boltzmann ◽

Energy Perturbation

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Calculation of relative binding affinities of fructose 1,6-bisphosphatase mutants with adenosine monophosphate using free energy perturbation method

Journal of Computational Chemistry ◽

10.1002/jcc.20617 ◽

2007 ◽

Vol 28 (5) ◽

pp. 932-937 ◽

Cited By ~ 8

Author(s):

Ravichandra Mutyala ◽

R. N. Reddy ◽

M. Sumakanth ◽

P. Reddanna ◽

M. Rami Reddy

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Adenosine Monophosphate ◽

Free Energy Perturbation ◽

Binding Affinities ◽

Relative Binding ◽

Fructose 1,6 Bisphosphatase ◽

Energy Perturbation

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Computational Prediction of Molecular Hydration Entropy with Hybrid Scaled Particle Theory and Free-Energy Perturbation Method

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.5b00325 ◽

2015 ◽

Vol 11 (10) ◽

pp. 4933-4942 ◽

Cited By ~ 9

Author(s):

Hwanho Choi ◽

Hongsuk Kang ◽

Hwangseo Park

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Computational Prediction ◽

Free Energy Perturbation ◽

Scaled Particle Theory ◽

Particle Theory ◽

Energy Perturbation

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Calculation of Absolute Protein–Ligand Binding Constants with the Molecular Dynamics Free Energy Perturbation Method

Methods in Molecular Biology - Molecular Modeling of Proteins ◽

10.1007/978-1-59745-177-2_6 ◽

2008 ◽

pp. 109-120 ◽

Cited By ~ 7

Author(s):

Hyung-June Woo

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Ligand Binding ◽

Perturbation Method ◽

Binding Constants ◽

Free Energy Perturbation ◽

Energy Perturbation

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Relative Binding Affinities of Fructose-1,6-Bisphosphatase Inhibitors Calculated Using a Quantum Mechanics-Based Free Energy Perturbation Method

Journal of the American Chemical Society ◽

10.1021/ja072905j ◽

2007 ◽

Vol 129 (30) ◽

pp. 9296-9297 ◽

Cited By ~ 27

Author(s):

M. Rami Reddy ◽

Mark D. Erion

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Perturbation Method ◽

Free Energy Perturbation ◽

Binding Affinities ◽

Relative Binding ◽

Fructose 1,6 Bisphosphatase ◽

Energy Perturbation

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