Structure Prediction
AlphaFold3 reproduction, predict protein/nucleic acid/small molecule complexes
Wohlwend et al.
Accurate and quick protein structure prediction for multimers and monomers
DeepMind et al. + ColabFold
Chai Discovery team
Predicts protein, DNA, RNA, and ligand complexes
Candido et al. 2026
Predict protein/nucleic acid/small molecule complexes. Outperforms AlphaFold3 with major gains on antibody-antigen interfaces.
Bytedance
OpenFold3 team
Antibody, Nanobody and TCR structure prediction
Abanades et al.
AlphaFold3 reproduction
Corley et al.
Modified AlphaFold for higher accuracy multimer structure prediction
Kalakoti et al.
Fast antibody structure, developability, and embeddings
Ellmen et al.
Antibody structure prediction
Kenlay et al.
Antibody conformational ensemble prediction
Spoendlin et al.
Cyclic peptide structure prediction
Rettie et al.
AlphaFold fine tuned with a flow matching objective
Jing et al.
Predict T Cell Receptor structures
Yin R et al.
Predicting multiple conformations via sequence clustering
Wayment-Steele et al.
Unified model for biomolecular cofolding (protein/RNA/DNA/ligand), binder filtering (iCS/ipSAE), and de novo binder design (minibinders + VHH nanobodies)
Fine-tuned AlphaFold for high-precision MHC–peptide complex prediction
Glukhov E et al.
Peptide-MHC complex structure prediction and peptide design.
Asgary AH et al.
Structure prediction with multimeric templates
Mirabello et al.
Protein complex structure prediction conditioned on experimental restraints (XL-MS, interface residues)
Xie et al.
Protein complex structure prediction from crosslinking mass-spectrometry restraints (XL-MS)
Stahl et al.
Predict protein structure given a sequence
Lin et al.
Predict protein conformations with subsampled AlphaFold2
Monteiro da Silva et al.
Predict protein structure without MSA
Wu et al.
Generates diverse protein structures using reduced MSA AlphaFold2
AlphaFold2-RAVE: From sequence to Boltzmann ensemble et al.
RNA foundation model for sequence embeddings and secondary structure prediction
Chen et al.
Nanobody structure prediction with HCDR3 blueprint and disulphide priors
Ali M et al.
Boltz-1 structure prediction guided by a cryo-EM density map
Raghu et al.
Density-map-guided refinement of a structure into a conformational ensemble (X-ray or cryo-EM; Boltz backends)
Chrispens et al.
End-to-end structure prediction of large protein complexes: AlphaFold-Multimer on subunit pairs plus combinatorial assembly, from sequence
Shor et al.