Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods

Reviews in Computational Chemistry ◽

10.1002/9780470125786.ch8 ◽

2007 ◽

pp. 295-320 ◽

Author(s):

Terry P. Lybrand

Keyword(s):

Molecular Dynamics ◽

Computer Simulation ◽

Free Energy ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Biomolecular Systems ◽

Energy Perturbation

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Application of molecular dynamics and free energy perturbation methods to metalloporphyrin-ligand systems ii: Co and dioxygen binding to myoglobin

Protein Science ◽

10.1002/pro.5560021119 ◽

1993 ◽

Vol 2 (11) ◽

pp. 1975-1986 ◽

Author(s):

Marco A. Lopez ◽

Peter A. Kollman

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Energy Perturbation

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Application of molecular dynamics and free energy perturbation methods to metalloporphyrin-ligand systems. I. Carbon monoxide and dioxygen binding to four heme systems

Journal of the American Chemical Society ◽

10.1021/ja00198a036 ◽

1989 ◽

Vol 111 (16) ◽

pp. 6212-6222 ◽

Author(s):

Marco A. Lopez ◽

Peter A. Kollman

Keyword(s):

Molecular Dynamics ◽

Carbon Monoxide ◽

Free Energy ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Energy Perturbation

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An approach to the application of free energy perturbation methods using molecular dynamics: applications to the transformations of methanol .fwdarw. ethane, oxonium .fwdarw. ammonium, glycine .fwdarw. alanine, and alanine .fwdarw. phenylalanine in aqueous solution and to H3O+(H2O)3 .fwdarw. NH4+(H2O)3 in the gas phase

Journal of the American Chemical Society ◽

10.1021/ja00240a001 ◽

1987 ◽

Vol 109 (6) ◽

pp. 1607-1614 ◽

Author(s):

U. C. Singh ◽

Frank K. Brown ◽

Paul A. Bash ◽

Peter A. Kollman

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Free Energy ◽

Gas Phase ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Energy Perturbation

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Accurate Calculations of Relative Melting Temperatures of Mutant Proteins by Molecular Dynamics/Free Energy Perturbation Methods

Biological Systems Under Extreme Conditions ◽

10.1007/978-3-662-04802-3_7 ◽

2002 ◽

pp. 139-165 ◽

Author(s):

Minoru Saito

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Mutant Proteins ◽

Melting Temperatures ◽

Energy Perturbation

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Modeling of novel CDK7 inhibitors activity by molecular dynamics and free energy perturbation methods

Mendeleev Communications ◽

10.1016/j.mencom.2020.07.008 ◽

2020 ◽

Vol 30 (4) ◽

pp. 430-432

Author(s):

Polina V. Rusina ◽

Ilya Yu. Titov ◽

Maria V. Panova ◽

Victor S. Stroylov ◽

Yana R. Abdyusheva ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Energy Perturbation

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ChemInform Abstract: An Approach to the Application of Free Energy Perturbation Methods Using Molecular Dynamics: Applications to the Transformations of CH3OH → CH3CH3, H3O+ → NH+ 4, Glycine → Alanine, and Alanine → Phenylalanine in Aqueous Solution and t

10.1002/chin.198730038 ◽

1987 ◽

Vol 18 (30) ◽

Author(s):

U. C. SINGH ◽

F. K. BROWN ◽

P. A. BASH ◽

P. A. KOLLMAN

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Free Energy ◽

Perturbation Methods ◽

Free Energy Perturbation ◽

Energy Perturbation

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The Use of Molecular Dynamics and Free Energy Perturbation Approaches in Simulating the Properties of Macromolecules and Their Binding to Ligands

Crystallographic and Modeling Methods in Molecular Design ◽

10.1007/978-1-4612-3374-9_8 ◽

1990 ◽

pp. 114-122

Author(s):

Peter A. Kollman

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Free Energy Perturbation ◽

Energy Perturbation

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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 ◽

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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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 ◽

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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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 ◽

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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