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

Autodock Vina

Protein-ligand docking

J. Eberhardt et. al

DiffDock

Protein-ligand docking with diffusion models

Corso et. al

Smina

Modified AutoDock, (unconventional) small molecule docking

Koes 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