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
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
Predict protein/nucleic acid/small molecule complexes, matching or surpassing AlphaFold 3
Qiao et. al
Antibody, Nanobody and TCR structure prediction
Abanades et. al
AlphaFold3 reproduction
Corley et. al
Given a density map and a protein sequence automatically build a model for it
Jamali et. al
Su 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
AlphaFold2-derived diffusion model for protein-protein docking. Upload receptor and ligand structures; outputs docked PDBs and ipTM scores per sample.
Liu 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)
Glukhov E 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
Predict protein structure given a sequence
Lin et. al
Predict protein conformations with subsampled AlphaFold2
Monteiro da Silva et. al
Multiple sequence alignment (MSA)
Steinegger 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
Predict conformational flexibility of antibody and TCR CDR3 loops
Motif-conditioned functional enzyme sequence and structure co-design
Song et al.
Structure-based TCR design for peptide-MHC targets
Bradley 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
Combinatorial assembly of large protein complexes from AlphaFold-Multimer subcomplex predictions
Shor et. al