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protein-structure

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UpdatedJuly 1, 2026 at 10:02

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.

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JWM0203

JWM0203/Claude-Science-for-win

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Biological Scientists, All OtherLife, Physical, and Social Science Occupations·SOC 19-1029

SKILL.md

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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

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

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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.

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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

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