GROMACS

Simulate protein only or protein-ligand interactions using GROMACS force field

H.J.C. Berendsen et al.

Membrane Protein MD (GROMACS)

Simulate membrane proteins embedded in lipid bilayers using GROMACS with CHARMM36 force field

Abraham et al.

AI2BMD

Ab initio accuracy molecular dynamics for proteins, using a machine-learned potential

Wang T. et al.

OpenMM MD

Simulate protein only or protein-ligand interactions using AMBER force field

Arantes P.R. et al.

ABB4-STEROIDS

Antibody conformational ensemble prediction

Spoendlin et al.

BioEmu

Approximate equilibrium distribution

Lewis et al.

MM/GB(PB)SA

Calculate protein-ligand or protein-protein binding free energy using Molecular mechanics/Generalized-Born (Poisson-Boltzmann) surface area

GIST

Per-voxel water thermodynamics around a binding site via GIST (cpptraj) over an explicit-solvent MD trajectory

Nguyen CN et al.

PDBFixer

Fix and prepare PDB structures for downstream simulation

Eastman P et al.

Relative Binding Free Energy

Relative energy of protein-ligand complexes

The OpenFE development team et al.

Membrane Relative Binding Free Energy

Relative binding free energy for membrane-embedded proteins

The OpenFE development team et al.

Absolute Binding Free Energy

Absolute binding free energy of protein-ligand complexes (net-neutral ligands only; use RBFE for charged ligands)

The OpenFE development team et al.

GroScore

Protein-protein binding affinity from steered MD

Perthold et al.

Orb Models 3

Protein ligand interaction energy

Rhodes et al.

MDGen

Generative modeling of molecular dynamics trajectories

Jing et al.

OpenFE

Alchemical free energy calculations (RBFE, ABFE, RHFE, SepTop, membrane RBFE) plus complex MD, with configurable temperature, force field, sampling, and solvent.

The OpenFE development team et al.

TMD

Differentiable molecular dynamics engine for RBFE calculations with GPU-accelerated HREX sampling

TMD Industries et al.

AF2Rave

Generates diverse protein structures using reduced MSA AlphaFold2

AlphaFold2-RAVE: From sequence to Boltzmann ensemble et al.

OpenMM Protein Relaxation

Relax a protein structure using OpenMM

P. Eastman et al.

g_mmpbsa

Estimate binding free energy (ΔGbind) from protein-ligand or protein-protein trajectories.

Kumari R. et al.

SSTMap

Water thermodynamics from an explicit-solvent MD trajectory: discrete hydration-site (HSA) energetics and entropy plus grid-based (GIST) solvation maps.

Haider K. et al.

OpenMM Metadynamics

Efficiently explore free energy landscapes for conformational changes, protein-ligand binding, and other biophysical processes using well-tempered metadynamics.

Tribello G.A. et al.

OpenMM Temperature Replica Exchange

Perform temperature replica exchange molecular dynamics for enhanced conformational sampling

Eastman P et al.

DynamicsPLM Finetuning

Finetune a dynamics-aware protein language model on your data

Kalifa et al.

Dyna-1

Predict millisecond conformational exchange

Wayment-Steele et al.