Protein Protein Docking
AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes
Wohlwend et al.
Accurate and quick protein structure prediction for multimers and monomers
Mirdita et al. (ColabFold) + Jumper et al. (AlphaFold2)
Chai Discovery team
Predict protein/nucleic acid/small molecule complexes, matching or surpassing AlphaFold 3 on interfaces
OpenDDE Project et al.
Predict protein/nucleic acid/small molecule complexes. Outperforms AlphaFold3 with major gains on antibody-antigen interfaces.
Bytedance
OpenFold3 team
Predict protein/nucleic acid/small molecule complexes, matching or surpassing AlphaFold 3
Qiao et al.
AlphaFold3 reproduction
Corley et al.
Protein-protein docking using inverted AlphaFold
Feng et al.
Rigid body protein-protein docking
Ganea et al.
Deep learning protein-protein docking with SE(3) equivariance
Ghani et al.
AlphaFold2-derived diffusion model for protein-protein docking. Upload receptor and ligand structures; outputs docked PDBs and ipTM scores per sample.
Liu et al.
Calculate protein-ligand or protein-protein binding free energy using Molecular mechanics/Generalized-Born (Poisson-Boltzmann) surface area
Binding ddG prediction of protein complexes
Shan et al.
Protein-protein binding affinity prediction for multiple complexes
Qian et al.
Evaluate your docking interface
Basu et al.
Score and rank antibody-antigen complex models by predicted DockQ
Xu et al.
Predict PPI of structures or sequences
Hu et al.
Predict antibody-antigen binding affinity
Jin et al. et al.
Molecular surface interaction fingerprints.
Gainza et al.
Predict DockQ score of a predicted protein structure
Bryant et al.
Scoring function for interprotein interactions in AlphaFold
Dunbrack et al.
Protein-protein docking using diffusion and flow matching
Lee et al.
Contact molecular surface area for protein-protein interfaces
Lawrence MC et al.
End-to-end structure prediction of large protein complexes: AlphaFold-Multimer on subunit pairs plus combinatorial assembly, from sequence
Shor et al.