adaptyvbioOfficial·21 Agent Skills Included

protein-design-skills

End-to-end computational protein binder design and validation

Guides complete protein binder design campaigns from target preparation through backbone generation, sequence design, structure validation, and quality filtering. Covers tools like RFdiffusion, BoltzGen, BindCraft, ProteinMPNN, Chai, and AlphaFold with research-backed QC thresholds and cost estimates. Eliminates guesswork in tool selection, hotspot picking, and experimental validation planning.

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npx skills add adaptyvbio/protein-design-skills --all -g -y

All Skills in This Repository (21)

Pure Emerald Level Indicators

📦 In Repo

adaptyvbio

binder-design

Guide researchers in selecting protein binder design tools via a decision-tree workflow.

binding-characterization

Guide SPR or BLI selection and troubleshoot binding-kinetics experiments.

chai

Predict protein structures from FASTA sequences using Chai-1.

protein-design-workflow

Plan protein design workflows from target preparation to validation.

foldseek

Search protein structures against PDB and AlphaFold databases with Foldseek.

protein-qc

Automate protein design quality-control checks with standardized thresholds and composite scoring.

esm

Compute protein embeddings and PLL scores using the ESM2 language model.

rfdiffusion

Generate protein backbones with RFdiffusion using contigmap and hotspot specifications.

setup

Guide users through installing Modal CLI, authenticating, and validating protein design environments.

solublempnn

Design solubility-optimized protein sequences for given backbones using soluble model weights.

bindcraft

Automate end-to-end binder design with BindCraft and AF2 validation.

boltz

Predict protein complex structures with Boltz-1/Boltz-2 and output CIF models.

Official

Advanced

Frequently Asked Questions

FAQPage Schema

How to install protein-design-skills?▼

Run `npx skills add adaptyvbio/protein-design-skills --all -g -y` in your terminal to install all 24 skills globally.

How to design a protein binder with AI?▼

Describe your target (e.g. a PDB ID) and the agent picks the right pipeline, such as BoltzGen or RFdiffusion for design, Chai for validation, and protein-qc for filtering.

Which binder design tool should I use?▼

The binder-design skill compares BoltzGen, BindCraft, RFdiffusion, and Mosaic by hit-rate, cost per design, and target type so you pick the best starting point.

Do I need a GPU to run these protein design skills?▼

Most heavy compute runs on Modal cloud GPUs with a free monthly credit tier, so you only need the Modal CLI and the biomodals repo set up locally.

Can I use these skills without structural biology experience?▼

Yes. The workflow and campaign-manager skills walk you through each pipeline step, thresholds, and troubleshooting in plain language.