Protein Ligand Docking
AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes
Wohlwend et. al
Chai Discovery team
Predicts protein, nucleic acid, and small-molecule complexes. AlphaFold3-level model with strong performance on protein–protein and antibody–antigen interfaces.
Bytedance
OpenFold3 team
Predict protein/nucleic acid/small molecule complexes, matching or surpassing AlphaFold 3
Qiao et. al
Protein-ligand docking
Anishchenko et. al
J. Eberhardt et. al
Protein-ligand docking with diffusion models
Corso et. al
Surface-informed diffusion model for protein-ligand docking
Cao et. al
Modified AutoDock, (unconventional) small molecule docking
Koes et. al
State of the art protein-ligand docking
Alcaide et. al
High-throughput ligand screening powered by QuickVina2 and AFVS
Calculate protein-ligand or protein-protein binding free energy using Molecular mechanics/Generalized-Born (Poisson-Boltzmann) surface area
Protein ligand docking and affinity prediction
Morehead et. al
Detect pockets on a protein
Guilloux et. al
Predict ligand binding sites
Gazizov et. al
Relative energy of protein-ligand complexes
Scheen J et. al
(Re)Generate a binding pocket for a given small molecule
Zhang et. al
Protein ligand interaction energy
Rhodes et. al
GNN-based protein-ligand binding affinity prediction with language model embeddings
Graber et. al
Protein-ligand binding affinity prediction from 3D structure
Valsson et. al