Boltz-2

AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes

Wohlwend et. al

Chai-1

AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes

Chai Discovery team

Protenix

AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes

Bytedance

IntFold

AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes

Qiao et. al

PLACER

Protein-ligand docking

Anishchenko et. al

DiffDock

Protein-ligand docking with diffusion models

Corso et. al

Smina

Modified AutoDock, (unconventional) small molecule docking

Koes et. al

GNINA

Molecular docking with deep learning

McNutt et. al

Unimol DockingV2

State of the art protein-ligand docking

Alcaide et. al

MM/GB(PB)SA

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

FlowDock

Protein ligand docking and affinity prediction

Morehead et. al

Relative Binding Free Energy

Relative energy of protein-ligand complexes

Scheen J et. al

RosettaFold All-Atom

Use RosettaFold to predict complexes of proteins, nucleic acids, and small molecules

Krishna R et. al