Free energy perturbation (FEP)-guided scaffold hopping

Scaffold Hopping ◽

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 ◽

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

Journal of Chemical Theory and Computation ◽

10.1021/ct800011m ◽

2008 ◽

Vol 4 (6) ◽

pp. 869-876 ◽

Cited By ~ 187

Author(s):

William L. Jorgensen ◽

Laura L. Thomas

Keyword(s):

Free Energy ◽

Chemical Equilibria ◽

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 ◽

Quantum Mechanical ◽

Quantum Mechanical Calculations ◽

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 ◽

Energy Calculation ◽

Binding Free Energy Calculation ◽

Free energy perturbation studies on inhibitor binding to HIV-1 proteinase

Journal of the American Chemical Society ◽

10.1021/ja00038a001 ◽

1992 ◽

Vol 114 (12) ◽

pp. 4447-4452 ◽

Cited By ~ 44

Author(s):

B. G. Rao ◽

R. F. Tilton ◽

U. C. Singh

Keyword(s):

Free Energy ◽

Inhibitor Binding ◽

Energy Perturbation ◽

Hiv 1