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
Relative energy of protein-ligand complexes
Scheen J et. al
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
Efficiently explore free energy landscapes for conformational changes, protein-ligand binding, and other biophysical processes using well-tempered metadynamics.
Tribello G.A. et. al
Perform temperature replica exchange molecular dynamics for enhanced conformational sampling
Eastman P et. al