Molecular Dynamics
Simulate protein only or protein-ligand interactions using GROMACS force field
H.J.C. Berendsen et. al
Simulate membrane proteins embedded in lipid bilayers using GROMACS with CHARMM36 force field
Abraham et. al
Simulate protein only or protein-ligand interactions using AMBER force field
Arantes P.R. et. al
Add waters to protein
Kuang et. al
Antibody conformational ensemble prediction
Spoendlin et. al
Approximate equilibrium distribution
Lewis et. al
Calculate protein-ligand or protein-protein binding free energy using Molecular mechanics/Generalized-Born (Poisson-Boltzmann) surface area
Relative energy of protein-ligand complexes
Scheen J et. al
Protein ligand interaction energy
Rhodes et. al
Generative modeling of molecular dynamics trajectories
Jing et. al
Run different free energy protocols
The OpenFE development team et. al
Differentiable molecular dynamics engine for RBFE calculations with GPU-accelerated HREX sampling
TMD Industries et. al
Generates diverse protein structures using reduced MSA AlphaFold2
AlphaFold2-RAVE: From sequence to Boltzmann ensemble et. al
Relax a protein structure using OpenMM
P. Eastman 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
Finetune a dynamics-aware protein language model on your data
Kalifa et al.
Deep learning virtual screening pipeline combining GNN ligand prioritization, OpenMM protein refinement, and AutoDock Vina docking
Noor et. al