protein-structure

name	protein-structure
description	Protein structure & protein language models (mirrors Claude Science's protein structure/language-model skill). PDB/UniProt pull & compare structures, Biopython parsing, ESM sequence representation; structure prediction (OpenFold3/Boltz-2/Evo2) via BioNeMo placeholder (needs GPU/NVIDIA). Use for protein structure, PDB, structure comparison, protein language models.

protein-structure

Toolchain

• Locally reproducible: connectors/pdb.py (structure search/download), connectors/uniprot.py (sequences/annotation), Biopython (parsing/comparison), ESM (if installed, sequence representation).
• External access required (placeholder): structure prediction OpenFold3 / Boltz-2 and the Evo 2 sequence model via connectors/_gated.py::bionemo (needs NVIDIA_API_KEY or a local GPU deployment). When unconfigured, report "external access required" — do not return fake structures.

Standard workflow

1. Pull target structure/sequence from UniProt/PDB (record accession) -> inputs/.
2. Structure comparison / pocket analysis / sequence representation -> outputs/.
3. Prediction: run ESM sequence-level locally; structure prediction via bionemo (if configured), otherwise report unavailable.
4. Figures (structure render / metrics) via figure-maker.

Hard rules

• Distinguish experimental (PDB) from predicted structures; note source and confidence (pLDDT). Unavailable hosted models = say external access is required.