Solvation free energies via alchemical simulations: let's get honest about sampling, once more

Free energy perturbation (FEP) approaches with stratification have seen widespread and increasing use in computational studies of biologically relevant molecules.

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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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Solvation Free Energies of Small Amides and Amines from Molecular Dynamics/Free Energy Perturbation Simulations Using Pairwise Additive and Many-Body Polarizable Potentials

The Journal of Physical Chemistry ◽

10.1021/j100029a040 ◽

1995 ◽

Vol 99 (29) ◽

pp. 11575-11583 ◽

Cited By ~ 72

Author(s):

Yanbo Ding ◽

Dan N. Bernardo ◽

Karsten Krogh-Jespersen ◽

Ronald M. Levy

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Free Energy Perturbation ◽

Free Energies ◽

Many Body ◽

Energy Perturbation ◽

Solvation Free Energies

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Quantum‐mechanical calculations of solvation free energies. A combinedabinitiopseudopotential free‐energy perturbation approach

The Journal of Chemical Physics ◽

10.1063/1.463928 ◽

1992 ◽

Vol 97 (6) ◽

pp. 4264-4271 ◽

Cited By ~ 52

Author(s):

Nagarajan Vaidehi ◽

Tomasz Adam Wesolowski ◽

Arieh Warshel

Keyword(s):

Free Energy ◽

Free Energy Perturbation ◽

Quantum Mechanical ◽

Perturbation Approach ◽

Quantum Mechanical Calculations ◽

Free Energies ◽

Energy Perturbation ◽

Solvation Free Energies

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Solvation Free Energies of Amino Acids Calculated by Molecular Dynamics/Free Energy Perturbation Method.

Chemical and Pharmaceutical Bulletin ◽

10.1248/cpb.43.717 ◽

1995 ◽

Vol 43 (5) ◽

pp. 717-721

Author(s):

Noriyuki YAMAOTSU ◽

Ikuo MORIGUCHI ◽

Shuichi HIRONO

Keyword(s):

Molecular Dynamics ◽

Amino Acids ◽

Free Energy ◽

Perturbation Method ◽

Free Energy Perturbation ◽

Free Energies ◽

Energy Perturbation ◽

Solvation Free Energies

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Relative solvation free energies calculated using an ab initio QM/MM-based free energy perturbation method: dependence of results on simulation length

Journal of Computer-Aided Molecular Design ◽

10.1007/s10822-009-9300-5 ◽

2009 ◽

Vol 23 (12) ◽

pp. 837-843 ◽

Cited By ~ 2

Author(s):

M. Rami Reddy ◽

Mark D. Erion

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Ab Initio ◽

Free Energy Perturbation ◽

Free Energies ◽

Energy Perturbation ◽

Solvation Free Energies

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Development of a Quantum Mechanics-Based Free-Energy Perturbation Method: Use in the Calculation of Relative Solvation Free Energies

Journal of the American Chemical Society ◽

10.1021/ja049281r ◽

2004 ◽

Vol 126 (20) ◽

pp. 6224-6225 ◽

Cited By ~ 20

Author(s):

M. Rami Reddy ◽

U. C. Singh ◽

Mark D. Erion

Keyword(s):

Free Energy ◽

Quantum Mechanics ◽

Perturbation Method ◽

Free Energy Perturbation ◽

Free Energies ◽

Energy Perturbation ◽

Solvation Free Energies

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Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

Journal of Chemical Theory and Computation ◽

10.1021/ct900587b ◽

2010 ◽

Vol 6 (5) ◽

pp. 1509-1519 ◽

Cited By ~ 733

Author(s):

Devleena Shivakumar ◽

Joshua Williams ◽

Yujie Wu ◽

Wolfgang Damm ◽

John Shelley ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Force Field ◽

Free Energy Perturbation ◽

Free Energies ◽

Energy Perturbation ◽

Solvation Free Energies

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Decomposition of the Solvation Free Energies of Deoxyribonucleoside Triphosphates Using the Free Energy Perturbation Method

The Journal of Physical Chemistry B ◽

10.1021/jp056623m ◽

2006 ◽

Vol 110 (25) ◽

pp. 12782-12788 ◽

Cited By ~ 61

Author(s):

Urban Bren ◽

Václav Martínek ◽

Jan Florián

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Free Energy Perturbation ◽

Free Energies ◽

Energy Perturbation ◽

Solvation Free Energies

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Crown ether-neutral molecule interactions studied by molecular mechanics, normal mode analysis, and free energy perturbation calculations. Near quantitative agreement between theory and experimental binding free energies

Journal of the American Chemical Society ◽

10.1021/ja00193a042 ◽

1989 ◽

Vol 111 (11) ◽

pp. 4046-4051 ◽

Cited By ~ 57

Author(s):

Peter D. J. Grootenhuis ◽

Peter A. Kollman

Keyword(s):

Free Energy ◽

Crown Ether ◽

Normal Mode Analysis ◽

Quantitative Agreement ◽

Mode Analysis ◽

Free Energy Perturbation ◽

Free Energies ◽

Energy Perturbation ◽

Molecule Interactions ◽

Binding Free Energies

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Direct Comparison of Experimental and Calculated Folding Free Energies for Hydrophobic Deletion Mutants of Chymotrypsin Inhibitor 2: Free Energy Perturbation Calculations Using Transition and Denatured States from Molecular Dynamics Simulations of Unfolding†

Biochemistry ◽

10.1021/bi0022036 ◽

2001 ◽

Vol 40 (9) ◽

pp. 2723-2731 ◽

Cited By ~ 37

Author(s):

YongPing Pan ◽

Valerie Daggett

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Free Energy Perturbation ◽

Deletion Mutants ◽

Free Energies ◽

Chymotrypsin Inhibitor ◽

Chymotrypsin Inhibitor 2 ◽

Energy Perturbation ◽

Dynamics Simulations ◽

Denatured States

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