AlphaFold
Accurate and quick protein structure prediction for multimers and monomers
Mirdita et al. (ColabFold) + Jumper et al. (AlphaFold2)
Structure Prediction
Chai-1
AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes
Chai Discovery team
Structure Prediction
ESMFold2
Predicts protein, DNA, RNA, and ligand complexes
Candido et al. 2026
Structure Prediction
OpenDDE
Predict protein/nucleic acid/small molecule complexes, matching or surpassing AlphaFold 3 on interfaces
OpenDDE Project et al.
Structure Prediction
Mol-1
Predict protein, nucleic acid, and small molecule complexes with an all-atom co-folding model
Molence Bio. "Mol-1: Open Frontier Biomolecular Intelligence" et al.
Structure Prediction
OpenFold3 (NVIDIA NIM)
OpenFold3 served by the NVIDIA BioNeMo NIM. Predict protein/nucleic acid/small molecule complexes.
OpenFold3 team / NVIDIA BioNeMo
Structure Prediction
Boltz-2 (NVIDIA NIM)
Boltz-2 served by the NVIDIA BioNeMo NIM. Complex structure prediction with optional binding affinity.
Boltz-2 / NVIDIA BioNeMo
Structure Prediction
AlphaFold2-Multimer (NVIDIA NIM)
DeepMind AlphaFold2-Multimer served by the NVIDIA BioNeMo NIM.
AlphaFold2-Multimer / NVIDIA BioNeMo
Structure Prediction
Protenix-v2
Predict protein/nucleic acid/small molecule complexes. Outperforms AlphaFold3 with major gains on antibody-antigen interfaces.
Bytedance
Structure Prediction
OpenFold3
AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes
OpenFold3 team
Structure Prediction
SoupFold
Fuse the pair representations of co-folding models (ESMFold2, OpenDDE, Protenix) to predict protein and protein-ligand complexes, reported by its authors to be more accurate than either alone
Jang H et al.
Structure Prediction
OpenBind
Open co-folding model tuned for protein-ligand complexes, built on OpenFold3
OpenBind Consortium
Structure Prediction
Prompteina
Text-conditioned all-atom protein generation and binder design
Lee et al.
Protein Design
IntelliFold 2
Predict protein/nucleic acid/small molecule complexes, matching or surpassing AlphaFold 3
Qiao et al.
Structure Prediction
ImmuneBuilder
Antibody, Nanobody and TCR structure prediction
Abanades et al.
Structure Prediction
AFSample2
Modified AlphaFold for higher accuracy multimer structure prediction
Kalakoti et al.
Structure Prediction
FlashABB
Fast antibody structure, developability, and embeddings
Ellmen et al.
Structure Prediction
ABodyBuilder3
Antibody structure prediction
Kenlay et al.
Structure Prediction
ABB4-STEROIDS
Antibody conformational ensemble prediction
Spoendlin et al.
Structure Prediction
Highfold
Cyclic peptide structure prediction
Zhang et al.
Structure Prediction
PathFold
Predict a protein's folding pathway
Zhang et al.
Structure Prediction
BioEmu 2
Predict structures, sample ensembles, and propagate complexes in time
Microsoft Research AI for Science 2026
Molecular Dynamics
AlphaFlow
AlphaFold fine tuned with a flow matching objective
Jing et al.
Structure Prediction
TCRModel2
Predict T Cell Receptor structures
Yin R et al.
Structure Prediction
TCRdock
TCR:pMHC ternary structure prediction with fine-tuned AlphaFold2
Bradley P.
Structure Prediction
SwiftMHC
Fast peptide-MHC-I structure + binding-affinity prediction in one pass
Baakman C et al.
Structure Prediction
AF Cluster
Predicting multiple conformations via sequence clustering
Wayment-Steele et al.
Structure Prediction
SF-Cluster
Frustration-guided MSA subsampling for multi-conformer prediction
Chatterjee Lab + Leusch et al.
Structure Prediction
Promera
Unified model for biomolecular cofolding (protein/RNA/DNA/ligand), binder filtering (iCS/ipSAE), and de novo binder design (minibinders + VHH nanobodies)
Jing et al.
Structure Prediction
MHC-Diff
Diffusion-based peptide-MHC-I complex structure prediction
Frühbuß D et al.
Structure Prediction
MHC-Fine
Fine-tuned AlphaFold for high-precision MHC–peptide complex prediction
Glukhov E et al.
Structure Prediction
PMGen
Peptide-MHC complex structure prediction and peptide design.
Asgary AH et al.
Structure Prediction
AF Unmasked
Structure prediction with multimeric templates
Mirabello et al.
Structure Prediction
GRASP
Protein complex structure prediction conditioned on experimental restraints (XL-MS, interface residues)
Xie et al.
Structure Prediction
AlphaLink2
Protein complex structure prediction from crosslinking mass-spectrometry restraints (XL-MS)
Stahl et al.
Structure Prediction
ESMFold
Predict protein structure given a sequence
Lin et al.
Structure Prediction
AF-Traj
Predict protein conformations with subsampled AlphaFold2
Monteiro da Silva et al.
Structure Prediction
OmegaFold
Predict protein structure without MSA
Wu et al.
Structure Prediction
ESM3
Generative protein language model. Fill in masked positions of a sequence, optionally conditioned on a structure, or predict structure from sequence.
Hayes et al.
Protein Language Models
AF2Rave
Generates diverse protein structures using reduced MSA AlphaFold2
AlphaFold2-RAVE: From sequence to Boltzmann ensemble et al.
Molecular Dynamics
ViennaRNA
RNA accessibility for ASO site selection and isolated RNA/DNA secondary-structure thermodynamics.
Lorenz et al.
Structure Prediction
RNA-FM
RNA foundation model for sequence embeddings and secondary structure prediction
Chen et al.
Structure Prediction
NbForge
Nanobody structure prediction with HCDR3 blueprint and disulphide priors
Ali M et al.
Structure Prediction
CryoBoltz
Boltz-1 structure prediction guided by a cryo-EM density map
Raghu et al.
Structure Prediction
Sampleworks
Density-map-guided refinement of a structure into a conformational ensemble (X-ray or cryo-EM; Boltz backends)
Chrispens et al.
Structure Prediction
CombFold
End-to-end structure prediction of large protein complexes: AlphaFold-Multimer on subunit pairs plus combinatorial assembly, from sequence
Shor et al.
Structure Prediction
DeCAF
Fast all-atom cofolding: predict protein and protein-ligand complexes ~5x faster than Boltz-1.
Scarpellini et al.
Structure Prediction