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

ESMFold2

Predicts protein, DNA, RNA, and ligand complexes

Candido et al. 2026

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

ImmuneBuilder

Antibody, Nanobody and TCR structure prediction

Abanades et al.

RosettaFold-3

AlphaFold3 reproduction

Corley et al.

AFSample2

Modified AlphaFold for higher accuracy multimer structure prediction

Kalakoti et al.

FlashABB

Fast antibody structure, developability, and embeddings

Ellmen et al.

ABodyBuilder3

Antibody structure prediction

Kenlay et al.

ABB4-STEROIDS

Antibody conformational ensemble prediction

Spoendlin et al.

Highfold

Cyclic peptide structure prediction

Zhang et al.

PathFold

Predict a protein's folding pathway

Zhang et al.

BioEmu 2

Predict structures, sample ensembles, and propagate complexes in time

Microsoft Research AI for Science 2026

AlphaFlow

AlphaFold fine tuned with a flow matching objective

Jing et al.

TCRModel2

Predict T Cell Receptor structures

Yin R et al.

TCRdock

TCR:pMHC ternary structure prediction with fine-tuned AlphaFold2

Bradley P.

SwiftMHC

Fast peptide-MHC-I structure + binding-affinity prediction in one pass

Baakman C et al.

AF Cluster

Predicting multiple conformations via sequence clustering

Wayment-Steele et al.

SF-Cluster

Frustration-guided MSA subsampling for multi-conformer prediction

Chatterjee Lab + Leusch et al.

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.

MHC-Diff

Diffusion-based peptide-MHC-I complex structure prediction

Frühbuß D et al.

MHC-Fine

Fine-tuned AlphaFold for high-precision MHC–peptide complex prediction

Glukhov E et al.

PMGen

Peptide-MHC complex structure prediction and peptide design.

Asgary AH et al.

AF Unmasked

Structure prediction with multimeric templates

Mirabello et al.

GRASP

Protein complex structure prediction conditioned on experimental restraints (XL-MS, interface residues)

Xie et al.

AlphaLink2

Protein complex structure prediction from crosslinking mass-spectrometry restraints (XL-MS)

Stahl et al.

ESMFold

Predict protein structure given a sequence

Lin et al.

AF-Traj

Predict protein conformations with subsampled AlphaFold2

Monteiro da Silva et al.

OmegaFold

Predict protein structure without MSA

Wu et al.

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.

AF2Rave

Generates diverse protein structures using reduced MSA AlphaFold2

AlphaFold2-RAVE: From sequence to Boltzmann ensemble et al.

ViennaRNA

RNA accessibility and secondary-structure analysis for ASO / siRNA target-site selection (ViennaRNA folding engine).

Lorenz et al.

RNA-FM

RNA foundation model for sequence embeddings and secondary structure prediction

Chen et al.

NbForge

Nanobody structure prediction with HCDR3 blueprint and disulphide priors

Ali M et al.

CryoBoltz

Boltz-1 structure prediction guided by a cryo-EM density map

Raghu et al.

Sampleworks

Density-map-guided refinement of a structure into a conformational ensemble (X-ray or cryo-EM; Boltz backends)

Chrispens 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.