end-to-end-protein-design-workflow
End-to-end protein design pipeline guide across preparation, generation, validation, and filtering. Use this skill when: (1) Starting a new protein design project, (2) Need step-by-step workflow guidance, (3) Understanding the full design pipeline, (4) Planning compute resources and timelines, (5) Integrating multiple design tools. For tool selection, use binder-design-tool-selection. For QC thresholds, use protein-design-qc.
npx skills add BioTender-max/awesome-bio-agent-skills --skill end-to-end-protein-design-workflow --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# End-to-End Protein Design Workflow **Plain-language role**: Use this skill when you want the full pipeline, from target preparation through final QC. ## Standard binder design pipeline ### Overview ``` Target Preparation --> Backbone Generation --> Sequence Design | | | v v v (pdb skill) (rfdiffusion) (proteinmpnn) | | v v Structure Validation --> Filtering | | v v (alphafold2-multimer/chai1-structure-prediction) (protein-design-qc) ``` ## Phase 1: Target preparation ### 1.1 Obtain target structure ```bash # Download from PDB curl -o target.pdb "https://files.rcsb.org/download/XXXX.pdb" ``` ### 1.2 Clean and prepare ```python # Extract target chain # Remove waters, ligands if needed # Trim to binding region + 10A buffer ``` ### 1.3 Select hotspots - Choose 3-6 exposed residues - Prefer charged/aromatic (K, R, E, D, W, Y, F) - Check surface accessibility - Verify residue numbering **Output**: `target_prepared.pdb`, hotspot list ## Phase 2: Backbone generation ### Option A: RFdiffusion (diverse exploration) ```bash modal run modal_rfdiffusion.py \ --pdb target_prepared.pdb \ --contigs "A1-150/0 70-100" \ --hotspot "A45,A67,A89" \ --num-designs 500 ``` ### Option B: BindCraft (end-t
- Standard binder design pipeline
- Overview
- Phase 1: Target preparation
- 1.1 Obtain target structure
- 1.2 Clean and prepare
- 1.3 Select hotspots
- Phase 2: Backbone generation
- Option A: RFdiffusion (diverse exploration)
- Option B: BindCraft (end-to-end)
- Phase 3: Sequence design
- For RFdiffusion backbones
- Phase 4: Structure validation
- Predict complexes
- Phase 5: Filtering and selection
Download from PDB curl -o target.pdb "https://files.rcsb.org/download/XXXX.pdb" modal run modal_rfdiffusion.py \ modal run modal_bindcraft.py \ for backbone in backbones/*.pdb; do modal run modal_proteinmpnn.py \ done Prepare FASTA with binder + target modal run modal_colabfold.py \
What does the end-to-end-protein-design-workflow skill do?
End-to-end protein design pipeline guide across preparation, generation, validation, and filtering. Use this skill when: (1) Starting a new protein design project, (2) Need step-by-step workflow guidance, (3) Understanding the full design pipeline, (4) Planning compute resources and timelines, (5) Integrating multiple design tools. For tool selection, use binder-design-tool-selection. For QC thresholds, use protein-design-qc.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill end-to-end-protein-design-workflow --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.