Molecular Dynamics
Simulate protein only or protein-ligand interactions using GROMACS force field
H.J.C. Berendsen et. al
Simulate protein only or protein-ligand interactions using AMBER force field
Arantes P.R. et. al
Approximate equilibrium distribution
Lewis et. al
Calculating protein-ligand binding free energy using Molecular mechanics/Generalized-Born (Poisson-Boltzmann) surface area
Generative modeling of molecular dynamics trajectories
Jing et. al
Run different free energy protocols
The OpenFE development team et. al
Estimate binding free energy (ΔGbind) from protein-ligand or protein-protein trajectories.
Kumari R. et. al