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protein-structure

Retrieve experimental structures from RCSB PDB, predicted structures from AlphaFold DB, or parse PDB/mmCIF files in the local workspace.

Skill by phenixace

IndexedMIT★ 2
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Works with Claude Code, Claude apps, Codex, Cursor, Gemini CLI, GitHub Copilot, VS Code, OpenCode, Goose, Windsurf. Read the repository before you give any tool access to your data.

npx agentmarket install skill/phenixace-protein-structure

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About

Retrieve experimental structures from RCSB PDB, predicted structures from AlphaFold DB, or parse PDB/mmCIF files in the local workspace. Use when atom coordinates, chain composition, ligands, pLDDT, or structure-backed inspection are required; keep experimental evidence and prediction confidence distinct.

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Permissions

What this skill can do and what it asks for, from its SKILL.md. Checked Oct 25, 2026.

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Install scripts
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Runs as
Python package

Network hosts it talks to 1

  • codeload.github.com · found in install command

Files it touches

  • ~/.claude/skills/protein-structure

What's inside

Skill name
protein-structure
Description
Retrieve experimental structures from RCSB PDB, predicted structures from AlphaFold DB, or parse PDB/mmCIF files in the local workspace. Use when atom coordinates, chain composition, ligands, pLDDT, or structure-backed inspection are required; keep experimental evidence and prediction confidence distinct.
License
MIT
Instructions
11 lines in SKILL.md · view on GitHub

Before installing

  • Ships executable scripts

Files (4)

  • SKILL.md
  • openai.yaml · agents/
  • handler.py · scripts/
  • skill.json

SKILL.md (first lines)

# Protein Structure

Use `structure_fetch_pdb` for a four-character PDB identifier, `structure_fetch_alphafold` for an exact UniProt accession, and `structure_parse_workspace` for a `.pdb`, `.cif`, or `.mmcif` file already imported into the constrained workspace.

AlphaFold coordinates are predictions. Interpret B-factor values as pLDDT only for models retrieved through `structure_fetch_alphafold`: scores above 90 are very high local confidence, 70–90 confident, 50–70 low, and below 50 very low. pLDDT does not establish relative domain placement; direct the researcher to PAE for that question.

The AlphaFold artifact includes a directional PAE matrix when the official bounded JSON is available. Rows represent the scored residue and columns the residue used for alignment; lower Å values indicate greater confidence in their relative position. The matrix may be mean-downsampled into contiguous residue bins for display and must not be converted into automatic domain, interaction, or mechanism claims.

The parser reads the first model, removes water, preserves protein and ligand atoms, derives chain sequences from C-alpha residues, and returns an atom-level viewer artifact. Large structures may be sampled for rendering while retaining the full parsed atom count.

From phenixace/Molemo_WorkBench, MIT.

More from phenixace/Molemo_WorkBench

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Last commit (this folder)
Aug 29, 2026 (1 month ago)

From GitHub (fetched Oct 24, 2026).

Details

License
MIT
Repository
github.com/phenixace/Molemo_WorkBench
First seen
Oct 24, 2026
Last checked
Oct 24, 2026
Source
GitHubgithub-graphql

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Cite this page

protein-structure skill. Agent Mart. https://agentmart.dev/skills/phenixace-protein-structure (last updated 2026-10-24)