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

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 ◽

Cited By ~ 17

Author(s):

Peter L. Cummins ◽

Jill E. Gready

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Dihydrofolate Reductase ◽

Mechanical Model ◽

Ion Transfer ◽

Hydride Ion ◽

Transfer Step ◽

Energy Perturbation ◽

Hydride Ion Transfer

Computer-aided drug design: A free energy perturbation study on the binding of methyl-substituted pterins and N5-deazapterins to dihydrofolate reductase

Journal of Computer-Aided Molecular Design ◽

10.1007/bf00124361 ◽

1993 ◽

Vol 7 (5) ◽

pp. 535-555 ◽

Cited By ~ 18

Author(s):

Peter L. Cummins ◽

Jill E. Gready

Keyword(s):

Free Energy ◽

Drug Design ◽

Dihydrofolate Reductase ◽

Computer Aided Drug Design ◽

Computer Aided ◽

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 ◽

Cited By ~ 28

Author(s):

Peter L. Cummins ◽

K. Ramnarayan ◽

U. C. Singh ◽

Jill E. Gready

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Dihydrofolate Reductase ◽

Probing the salt bridge in the dihydrofolate reductase-methotrexate complex by using the coordinate-coupled free-energy perturbation method.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.85.12.4280 ◽

1988 ◽

Vol 85 (12) ◽

pp. 4280-4284 ◽

Cited By ~ 41

Author(s):

U. C. Singh

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Dihydrofolate Reductase ◽

Salt Bridge ◽

Free Energy Perturbation Calculations on Glucosidase-Inhibitor Complexes

Medicinal Chemistry ◽

10.2174/1573406054864151 ◽

2005 ◽

Vol 1 (5) ◽

pp. 455-460 ◽

Cited By ~ 4

Author(s):

F. Ruiz ◽

J. Grigera

Keyword(s):

Free Energy ◽

Glucosidase Inhibitor ◽

Free energy perturbation calculations on binding and catalysis after mutating threonine 220 in subtilisin

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)99028-9 ◽

1991 ◽

Vol 266 (18) ◽

pp. 11801-11809

Author(s):

N. Mizushima ◽

D. Spellmeyer ◽

S. Hirono ◽

D. Pearlman ◽

P. Kollman

Keyword(s):

Free Energy ◽

PyAutoFEP: An Automated Free Energy Perturbation Workflow for GROMACS Integrating Enhanced Sampling Methods

Journal of Chemical Theory and Computation ◽

10.1021/acs.jctc.1c00194 ◽

2021 ◽

Author(s):

Luan Carvalho Martins ◽

Elio A. Cino ◽

Rafaela Salgado Ferreira

Keyword(s):

Free Energy ◽

Sampling Methods ◽

Enhanced Sampling ◽

Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations

ACS Central Science ◽

10.1021/acscentsci.1c00039 ◽

2021 ◽

Vol 7 (3) ◽

pp. 467-475 ◽

Cited By ~ 1

Author(s):

Chun-Hui Zhang ◽

Elizabeth A. Stone ◽

Maya Deshmukh ◽

Joseph A. Ippolito ◽

Mohammad M. Ghahremanpour ◽

...

Keyword(s):

Free Energy ◽

Main Protease ◽

Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling

The Journal of Chemical Physics ◽

10.1063/1.1359181 ◽

2001 ◽

Vol 114 (17) ◽

pp. 7303-7311 ◽

Cited By ~ 116

Author(s):

Nandou Lu ◽

David A. Kofke

Keyword(s):

Free Energy ◽

Molecular Simulation ◽

Thrombin Inhibition by Novel Benzamidine Derivatives: A Free-Energy Perturbation Study

Journal of Medicinal Chemistry ◽

10.1021/jm020123p ◽

2002 ◽

Vol 45 (23) ◽

pp. 4995-5004 ◽

Cited By ~ 6

Author(s):

Cristiano Ruch Werneck Guimarães ◽

Ricardo Bicca de Alencastro

Keyword(s):

Free Energy ◽

Thrombin Inhibition ◽