bio-structure-annotation
Structure prediction and structure-based annotation.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-structure-annotation --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.
# Bio Structure Annotation Structure prediction and structure-based annotation. ## Instructions 1. Run a fast embedding screen with TM-Vec to triage candidate proteins by remote homology before incurring structure-prediction cost. 2. Predict structures on a GPU node. AlphaFold3 is intentionally not part of this stack (non-commercial license, large VRAM footprint, no clear quality gap for the workflows in this repo). Use: - **Boltz-2** (MIT license; CUDA; NVIDIA cuEquivariance kernels) as the default predictor — joint structure-and-affinity, ~1000× faster than FEP for binding-affinity estimation, comparable accuracy to AF3 on benchmarked complexes. - **ColabFold** v1.5.5+ with an **MMseqs2-GPU** MSA backend when a wider MSA than Boltz-2 builds is required (≈31.8× faster MSA generation versus the standard AF2 pipeline; *Nature Protocols* 2025, DOI: 10.1038/s41596-024-01060-5). - **ESMFold** for fast monomer pre-screening only (15–20 GB VRAM; lower accuracy than Boltz-2). 3. Search predicted or experimental structures with **Foldseek v9+**. Use `--gpu 1` on CUDA Turing or newer for the ProstT5-backed search (4–27× speedup). Consider Foldseek-Multimer when complex-vs-complex search is
- Instructions
- Quick Reference
- Input Requirements
- Output
- Quality Gates
- Examples
- Example 1: Expected input layout
- Troubleshooting
What does the bio-structure-annotation skill do?
Structure prediction and structure-based annotation.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bio-structure-annotation --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.