Protein Protein Docking
Boltz-2
AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes
Wohlwend et al.
AlphaFold
Accurate and quick protein structure prediction for multimers and monomers
Mirdita et al. (ColabFold) + Jumper et al. (AlphaFold2)
Chai-1
AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes
Chai Discovery team
OpenDDE
Predict protein/nucleic acid/small molecule complexes, matching or surpassing AlphaFold 3 on interfaces
OpenDDE Project et al.
OpenFold3 (NVIDIA NIM)
OpenFold3 served by the NVIDIA BioNeMo NIM. Predict protein/nucleic acid/small molecule complexes.
OpenFold3 team / NVIDIA BioNeMo
Boltz-2 (NVIDIA NIM)
Boltz-2 served by the NVIDIA BioNeMo NIM. Complex structure prediction with optional binding affinity.
Boltz-2 / NVIDIA BioNeMo
AlphaFold2-Multimer (NVIDIA NIM)
DeepMind AlphaFold2-Multimer served by the NVIDIA BioNeMo NIM.
AlphaFold2-Multimer / NVIDIA BioNeMo
Protenix-v2
Predict protein/nucleic acid/small molecule complexes. Outperforms AlphaFold3 with major gains on antibody-antigen interfaces.
Bytedance
OpenFold3
AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes
OpenFold3 team
SoupFold
Fuse ESMFold2 and OpenDDE to predict protein and protein-ligand complexes, reported by its authors to be more accurate than either alone
Jang H et al.
OpenBind
Open co-folding model tuned for protein-ligand complexes, built on OpenFold3
OpenBind Consortium
IntelliFold 2
Predict protein/nucleic acid/small molecule complexes, matching or surpassing AlphaFold 3
Qiao et al.
RAPiDock
All-atom protein-peptide docking with a diffusion generative model
Zhao et al.
RosettaFold-3
AlphaFold3 reproduction
Corley et al.
ColabDock
Protein-protein docking using inverted AlphaFold
Feng et al.
EquiDock
Rigid body protein-protein docking
Ganea et al.
GeoDock
Deep learning protein-protein docking with SE(3) equivariance
Chu et al.
AF2Dock
AlphaFold2-derived diffusion model for protein-protein docking. Upload receptor and ligand structures; outputs docked PDBs and ipTM scores per sample.
Liu et al.
MM/GB(PB)SA
Calculate protein-ligand or protein-protein binding free energy using Molecular mechanics/Generalized-Born (Poisson-Boltzmann) surface area
Binding ddG
Binding ddG prediction of protein complexes
Shan et al.
PPAP
Protein-protein binding affinity prediction for multiple complexes
Qian et al.
DockQ
Evaluate your docking interface
Basu et al.
FoldBench Evaluator
Score a predicted complex the way FoldBench does
Xu et al.
GroScore
Protein-protein binding affinity from steered MD
Perthold et al.
DeepRank-Ab
Score and rank antibody-antigen complex models by predicted DockQ
Xu et al.
Spatial PPI v2
Predict PPI of structures or sequences
Hu et al.
DSMBind
Predict antibody-antigen binding affinity
Jin et al. et al.
MaSIF
Molecular surface interaction fingerprints.
Gainza et al.
PDockQ
Predict DockQ score of a predicted protein structure
Bryant et al.
IPSAE
Scoring function for interprotein interactions in AlphaFold
Dunbrack et al.
DFMDock
Protein-protein docking using diffusion and flow matching
Lee et al.
DiffDock-PP
Rigid protein-protein docking that samples many candidate poses by diffusion and ranks them with a confidence model
Ketata et al.
Contact MS
Contact molecular surface area for protein-protein interfaces
Lawrence MC et al.
CombFold
End-to-end structure prediction of large protein complexes: AlphaFold-Multimer on subunit pairs plus combinatorial assembly, from sequence
Shor et al.
DeCAF
Fast all-atom cofolding: predict protein and protein-ligand complexes ~5x faster than Boltz-1.
Scarpellini et al.