By name: protein-design description: > Computational protein design toolkit. Use this skill group when: (1) Designing protein binders from scratch, (2) Predicting protein structures (Chai, Boltz, Protenix), (3) Sequence design with ProteinMPNN/LigandMPNN/SolubleMPNN, (4) Quality control and filtering of protein designs, (5) Planning and managing binder design campaigns, (6) Experimental characterization (SPR, BLI, cell-free expression), (7) Searching protein databases (PDB, UniProt, AFDB), (8) Antibody/nanobody design (IgGM, mBER).
This is the top-level index. Sub-skills handle specific tools. license: MIT category: orchestration tags: [protein-design, binder, structure-prediction, sequence-design, qc] source: https://github.com/adaptyvbio/protein-design-skills
Protein Design Skill Group
A comprehensive toolkit for computational protein design, adapted from adaptyvbio/protein-design-skills and hgbrian/biomodals.
Quick Decision Guide
"I want to design a binder"
→ Start with binder-design or campaign-manager
"I need to design proteins (all-atom)"
→ boltzgen (recommended) or bindcraft (integrated end-to-end)
"I have backbones, need sequences"
→ proteinmpnn, ligandmpnn (ligand), or solublempnn (E. coli expression)
"I need to validate my designs"
→ chai, boltz, or protenix (AF3-like)
"I need to rank/filter designs"
→ protein-qc for thresholds, ipsae for ranking
"I need a protein structure"
→ pdb (fetch), foldseek (structural search), uniprot (sequence)
"I need antibody/nanobody design"
→ iggm (antibody/nanobody CDRs) or mber (VHH mask-based)
"I need to express/test my protein"
→ cell-free-expression for CFPS, binding-characterization for SPR/BLI
"I'm just getting started"
→ setup first, then protein-design-workflow for the full pipeline
All Available Sub-Skills
Design Tools
| Skill | Description |
|---|---|
boltzgen |
All-atom binder design — recommended starting point |
bindcraft |
End-to-end binder design with integrated validation |
proteinmpnn |
General sequence design for existing backbones |
ligandmpnn |
Ligand/metal-aware sequence design |
solublempnn |
Solubility-optimized sequence design |
Structure Prediction
| Skill | Description |
|---|---|
chai |
Chai-1 structure prediction (protein, ligand, RNA) |
boltz |
Boltz-1 open-source AF3-like prediction |
protenix |
Protenix: ByteDance AF3 open reproduction |
esm |
ESM2 embeddings and sequence scoring |
Antibody / Nanobody
| Skill | Description |
|---|---|
iggm |
IgGM: generative model for antibody & nanobody CDR design |
mber |
mBER: VHH nanobody mask-based design |
Evaluation
| Skill | Description |
|---|---|
protein-qc |
QC metrics, thresholds, composite scoring |
ipsae |
ipSAE ranking (1.4× better than ipTM) |
Databases & Utilities
| Skill | Description |
|---|---|
pdb |
Fetch and prepare structures from RCSB PDB |
uniprot |
Protein sequence and annotation lookup |
foldseek |
Structural similarity search |
Experimental
| Skill | Description |
|---|---|
binding-characterization |
SPR/BLI experimental guidance |
cell-free-expression |
CFPS optimization and troubleshooting |
Orchestration
| Skill | Description |
|---|---|
binder-design |
Tool selection guidance |
campaign-manager |
Campaign planning and health assessment |
protein-design-workflow |
End-to-end pipeline guide |
setup |
First-time environment setup |