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protein-structure

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Aktualisiert1. Juli 2026 um 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.

Installation

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Quelle

JWM0203

JWM0203/Claude-Science-for-win

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Verwandte BerufeSOC

Basierend auf der SOC-Berufsklassifikation

Sonstige BiowissenschaftlerNatur- und Sozialwissenschaften·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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data-analysis

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Reproducible data analysis. Uses pandas/numpy/scipy/statsmodels for cleaning, statistics, and modeling; scripts and random seeds all land in the run, and every reported number is recomputable. Use to analyze tabular/matrix data, run statistical tests, or model.

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Publication-grade figures. Uses matplotlib to generate figures from a script (never hand-drawn, never pasted from an unknown source); each figure has a rerunnable script. Layer the global CCF-Figure skill for figure conventions / top-venue layout. Use to draw paper figures and iterate to publication quality.

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Provenance-backed literature review. Searches PubMed / Europe PMC / arXiv (connectors/literature.py), dedupes, synthesizes by theme, and attaches a DOI/PMID to every conclusion. Use when you need a literature review, evidence for a claim, or a related-work section.

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manuscript

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Manuscript writing and iteration to publication quality. Organizes IMRaD structure, inserts run-generated figures/tables, manages references, and produces docx/pdf/md. Layer the global docx / doc-coauthoring / pdf skills. Use to write a paper draft, methods, results, and iterate.

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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.