Molecular dynamics and free energy perturbation study of hydride-ion transfer step in dihydrofolate reductase using combined quantum and molecular mechanical model

Journal of Computational Chemistry ◽

10.1002/(sici)1096-987x(199806)19:8<977::aid-jcc15>3.0.co;2-4 ◽

1998 ◽

Vol 19 (8) ◽

pp. 977-988 ◽

Author(s):

Peter L. Cummins ◽

Jill E. Gready

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Dihydrofolate Reductase ◽

Mechanical Model ◽

Free Energy Perturbation ◽

Ion Transfer ◽

Hydride Ion ◽

Transfer Step ◽

Energy Perturbation ◽

Hydride Ion Transfer

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Molecular dynamics/free energy perturbation study on the relative affinities of the binding of reduced and oxidized NADP to dihydrofolate reductase

Journal of the American Chemical Society ◽

10.1021/ja00022a008 ◽

1991 ◽

Vol 113 (22) ◽

pp. 8247-8256 ◽

Author(s):

Peter L. Cummins ◽

K. Ramnarayan ◽

U. C. Singh ◽

Jill E. Gready

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Dihydrofolate Reductase ◽

Free Energy Perturbation ◽

Energy Perturbation

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Structural and energetic aspects of the reaction pathway and transition state for hydride-ion transfer in dihydrofolate reductase

Zurich, Switzerland, September 3–8, 1989 ◽

10.1515/9783110889000-144 ◽

1990 ◽

pp. 748-751

Keyword(s):

Transition State ◽

Dihydrofolate Reductase ◽

Reaction Pathway ◽

Ion Transfer ◽

Hydride Ion ◽

Hydride Ion Transfer

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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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A free-energy perturbation study of the binding of methotrexate to mutants of dihydrofolate reductase.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.85.24.9519 ◽

1988 ◽

Vol 85 (24) ◽

pp. 9519-9523 ◽

Author(s):

U. C. Singh ◽

S. J. Benkovic

Keyword(s):

Free Energy ◽

Dihydrofolate Reductase ◽

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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Insight into the specificity of thymidylate synthase from molecular dynamics and free energy perturbation calculations

Journal of the American Chemical Society ◽

10.1021/ja00132a022 ◽

1995 ◽

Vol 117 (27) ◽

pp. 7213-7227 ◽

Author(s):

Giulio Rastelli ◽

Bert Thomas ◽

Peter A. Kollman ◽

Daniel V. Santi

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Thymidylate Synthase ◽

Free Energy Perturbation ◽

Energy Perturbation ◽

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Importance of the proximity of solvation: molecular dynamics and free energy perturbation studies of [1 6 ]starand and its model with various alkali metal ions

Journal of Molecular Structure THEOCHEM ◽

10.1016/s0166-1280(99)00295-x ◽

2000 ◽

Vol 499 (1-3) ◽

pp. 111-119 ◽

Author(s):

Seung Joo Cho

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Alkali Metal ◽

Free Energy Perturbation ◽

Alkali Metal Ions ◽

Energy Perturbation

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Free Energy Perturbation and Molecular Dynamics Studies of [16]Starand with Various Alkali Metal Ions

The Journal of Organic Chemistry ◽

10.1021/jo982367g ◽

1999 ◽

Vol 64 (16) ◽

pp. 5787-5793 ◽

Author(s):

Seung Joo Cho ◽

Peter A. Kollman

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Alkali Metal ◽

Free Energy Perturbation ◽

Alkali Metal Ions ◽

Energy Perturbation

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