Protein Design
BindCraft2
Design binders for your target as miniproteins, antibodies, peptides or scaffolds
ESMFold2 Binder Design
Design de novo protein binders against a target
Candido et al. 2026
ProteinMPNN
Protein structure to sequence prediction
Dauparas et al.
BoltzGen
De novo binder design for nanobodies, antibodies, proteins, peptides, and cyclotides
BoltzGen et al.
Genie 3
De novo binder design
Lin et al.
RFpeptides
Design macrocyclic proteins
Rettie et al.
BindCraft
Design de novo binders for your target
Pacesa et al.
Odin-Multi
Multi-target binder design with counter-selection against off-targets
DigBioLab. 'Odin-Multi: multi-target AF2 binder hallucination with counter-selection'. https://github.com/DigBioLab/odin_multi et al.
FreeBindCraft
Open-source BindCraft variant with ipSAE scoring (no PyRosetta)
Pacesa et al.
Bindome BindCraft
Accelerated BindCraft: fixed-length binders, full-target context, ipSAE
Wenckstern et al.
Proteina-Complexa
Fully atomistic protein and ligand binder design
Didi et al.
NOS
Generate antibodies optimized for a given property
Gruver et al.
PepINVENT
Design peptides with non-natural amino acids by sampling masked CHUCKLES templates.
Geylan et al., arXiv 2024
PepMimic
Design peptide binders by mimicking a known binder's interface
Kong et al.
BetterMPNN Finetuning
Reinforcement-learning finetuning of ProteinMPNN against a structure-predictor reward, for one target
ShanghaiTech-iGEM 2025
SwitchCraft
Design proteins that switch shape in response to a ligand
Jing et al.
Proto
Constraint-based multi-objective sequence design (Proto optimizer)
Merchant et al.
RFdiffusion3
All atom protein design with atom-level and residue-level motif scaffolding
Butcher et al.
RFdiffusion2
Enzyme active site scaffolding with atom-level or residue-level motif specification
Ahern et al.
TiDE-Ab
Epitope-specific de novo antibody design
Kim et al.
Germinal
De novo antibody design
Santiago et al.
OpenGerminal
Open-source de novo antibody design
Han et al.
IgDesign
In vitro validated antibody design against antigens
Shanehsazzadeh et al.
PXDesign
De novo protein binder design using diffusion models
ByteDance et al.
FAMPNN
Protein structure to sequence design with full-atom packed outputs
Shuai et al.
AntiFold
Design sequences for antibodies
Hummer et al.
mBER
VHH binder design
Swanson et al.
Antibody Diffusion Properties
Design property-aware CDR sequence/structure
Villegas-Morcillo et al.
Antibody Evolution
Language models to recommend mutations for increased antibody binding affinity
Hie et al.
RFOptimization
Improve an existing binder by repeatedly redesigning and re-predicting it
Zhang O et al.
RFdiffusion
Design or diversify proteins
Watson et al.
FrameFlow
Motif scaffolding protein design
Yim et al.
ProteinMPNN-ddG
Predict stability of point mutations
Dutton et al.
AntiDIF
Antibody inverse folding
Branson et al.
ProteinMPNN-ddG Binder
Predict stability of point mutations
Dutton et al.
LigandMPNN
Inverse folding with modeling of small molecules and more
Dauparas et al.
PottsMPNN
Sequence design with Potts pairwise interactions
Birnbaum and Keating
Proton-PottsMPNN
pH-switchable binder design
Jacobsen et al.
BoltzDesign1
Invert Boltz-1 to design protein binders
Cho et al.
AnewOmni
All-atom generative design of small molecule, peptide, and antibody binders
Kong et al.
ZymCTRL
Conditionally generate artificial enzymes
Illanes-Vicioso et al.
All Atom Protein Design
Design ligand-binding proteins with RFdiffusion All Atom
Krishna et al.
Protein Hunter
De novo protein design
Cho et al.
EvoProtGrad
Generate mutations with directed evolution
Emami et al.
AfCycDesign
Redesign the sequence of an existing cyclic peptide structure
Rettie et al.
Structural Evolution
Mutate protein complexes with structure-informed language model
Varun R. Shanker et al. et al.
NA-MPNN
Sequence design for protein, RNA, DNA, and mixed-polymer structures; protein-DNA binding specificity prediction
Kubaney et al.
EvoPro
Genetic algorithm-based protein binder optimization pipeline
Goudy OJ et al.
PMGen
Peptide-MHC complex structure prediction and peptide design.
Asgary AH et al.
Dayhoff
Generate sequences conditioned on existing sequence
Kevin K. Yang et al.
Caliby
Potts model-based protein sequence design method that can condition on structural ensembles
Richard W. Shuai et al.
ProteinMPNN Score
Protein structure to sequence prediction
Dauparas et al.
RSO Binder Design
Efficient binder design
Frank et al.
PocketGen
(Re)Generate a binding pocket for a given small molecule
Zhang et al.
ColabDesign Fixed Backbone
Generate sequences given structure via reversing AlphaFold
Frank et al.
AbLang-MPNN
Hybrid antibody design using AbLang + ProteinMPNN ensemble
del Alamo et al.
AntiBERTy
Optimize antibody/nanobody sequence affinity
Ruffolo et al.
HyperMPNN
Design thermostable proteins
Ertelt et al.
AbMPNN
Antibody sequence design
Dreyer et al.
APM
All-Atom Protein Generative Model
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.
RiffDiff-ProtFlow
Generate backbone fragments from a theozyme to build a motif library
Braun et al.
ProteusAI
ML-assisted Directed Evolution
J. Funk et al.
ProtRL Steering
Steer a protein language model toward a family or a score as it writes new sequences
Garibbo et al.
EnzyGen2
Motif-conditioned functional enzyme sequence and structure co-design
Song et al.
MULTI-evolve
Model-guided directed evolution workflow for multi-mutant nomination and assembly design
Tran et al.
ADAPT
Structure-based TCR or antibody design for peptide-MHC targets
Motmaen et al.
Mosaic Hallucination
Gradient-based binder design using Boltz-2, Protenix, AlphaFold, or OpenDDE
Boyd et al.
CyclicMPNN
Design stable cyclic peptide sequences for a given backbone
Powers et al.
CoSiNE
Evolve antibody sequences along realistic affinity-maturation trajectories
Lu et al.
DynamicMPNN
Design sequences compatible with multiple conformational states
Abrudan et al.
ODesign Antibody
Antibody CDR design with ODesign all-atom generative model
Zhang et al.
DISCO
Diffusion-based protein sequence-structure co-design conditioned on ligands, DNA, or RNA
Rector-Brooks et al.
RFDpoly
Diffusion-based de novo design of RNA, DNA, and nucleoprotein complex structures
Favor et al.