Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics/Molecular Mechanics

2005 ◽  
Vol 109 (20) ◽  
pp. 10474-10483 ◽  
Author(s):  
Frauke Gräter ◽  
Sonja M. Schwarzl ◽  
Annick Dejaegere ◽  
Stefan Fischer ◽  
Jeremy C. Smith
Keyword(s):  
Quantum Mechanics ◽  
Ligand Binding ◽  
Molecular Mechanics ◽  
Free Energies ◽  
Binding Free Energies

scholarly journals Computation of protein–ligand binding free energies using quantum mechanical bespoke force fields

MedChemComm ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 1116-1120 ◽  
Author(s):  
Daniel J. Cole ◽  
Israel Cabeza de Vaca ◽  
William L. Jorgensen
Keyword(s):  
Ligand Binding ◽  
Force Field ◽  
Molecular Mechanics ◽  
Force Fields ◽  
Quantum Mechanical ◽  
T4 Lysozyme ◽  
Free Energies ◽  
Binding Free Energies

A quantum mechanical bespoke molecular mechanics force field is derived for the L99A mutant of T4 lysozyme and used to compute absolute binding free energies of six benzene analogs to the protein.

scholarly journals Protein-ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange-correlation functional

2021 ◽  
Author(s):  
Lennart Gundelach ◽  
Christofer S Tautermann ◽  
Thomas Fox ◽  
Chris-Kriton Skylaris
Keyword(s):  
Drug Discovery ◽  
Ligand Binding ◽  
Dft Calculations ◽  
Quantum Mechanical ◽  
Free Energies ◽  
Ligand Interaction ◽  
Exchange Correlation ◽  
Ligand Free ◽  
Protein Ligand Interaction ◽  
Binding Free Energies

The accurate prediction of protein-ligand binding free energies with tractable computational methods has the potential to revolutionize drug discovery. Modeling the protein-ligand interaction at a quantum mechanical level, instead of...

scholarly journals Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

2021 ◽  
Author(s):  
Yuriy Khalak ◽  
Gary Tresdern ◽  
Matteo Aldeghi ◽  
Hannah Magdalena Baumann ◽  
David L. Mobley ◽  
...  
Keyword(s):  
Free Energy ◽  
Drug Discovery ◽  
Drug Design ◽  
Ligand Binding ◽  
Binding Free Energy ◽  
Free Energy Calculations ◽  
Free Energies ◽  
Energy Calculations ◽  
Binding Free Energy Calculations ◽  
Binding Free Energies

The recent advances in relative protein-ligand binding free energy calculations have shown the value of alchemical methods in drug discovery. Accurately assessing absolute binding free energies, although highly desired, remains...

Receptor–Ligand Binding Free Energies from a Consecutive Histograms Monte Carlo Sampling Method

2020 ◽  
Vol 16 (10) ◽  
pp. 6645-6655
Author(s):  
Hao Liu ◽  
Jianpeng Deng ◽  
Zhou Luo ◽  
Yawei Lin ◽  
Kenneth M. Merz ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Sampling Method ◽  
Monte Carlo Sampling ◽  
Free Energies ◽  
Receptor Ligand ◽  
Binding Free Energies

A water-swap reaction coordinate for the calculation of absolute protein–ligand binding free energies

2011 ◽  
Vol 134 (5) ◽  
pp. 054114 ◽  
Author(s):  
Christopher J. Woods ◽  
Maturos Malaisree ◽  
Supot Hannongbua ◽  
Adrian J. Mulholland
Keyword(s):  
Ligand Binding ◽  
Reaction Coordinate ◽  
Free Energies ◽  
Binding Free Energies
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