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
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Install
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.
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About
Reviews
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Permissions
What this skill can do and what it asks for, from its SKILL.md. Checked Oct 25, 2026.
- Tools
- No tools found
- Secrets
- None asked for
- Install scripts
- None found
- 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.
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Signals
- Stars
- 2
- Forks
- 0
- Open issues
- 0
- Last commit (this folder)
- Aug 29, 2026 (2 months 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
More from phenixace
- 0.557score
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phenixace
Turn molecular and protein analysis results into declarative property charts and residue-level sequence tracks.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
guided-workflows
phenixace
Create reviewable, researcher-approved plans from Molemo scientific tools.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
hmmer-profile-search
phenixace
Validate and run bounded local HMMER3 profile-to-protein searches with domain coordinates, explicit thresholds, researcher approval and auditable outputs.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
research-router
phenixace
Route broad life-science research questions to the smallest useful set of Molemo skills.
SkillBFreshness: B★ 2Claude Code +9 - 0.557score
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phenixace
Review source-linked ChEMBL small-molecule activity evidence for an exact UniProt single-protein target.
SkillBFreshness: B★ 2Claude Code +9 - 0.554score
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Retrieve named compounds from PubChem and protein records from UniProt using fixed official API hosts.
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protein-structure skill. Agent Mart. https://agentmart.dev/skills/phenixace-protein-structure (last updated 2026-10-24)