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Agent skill

Alphafold DB

by aipoch in aipoch/medical-research-skills

Access over 200M protein structures from AlphaFold DB; use when you need to retrieve predicted 3D structures (PDB/mmCIF), confidence metrics (pLDDT/PAE), or protein metadata by UniProt accession.

MITAuto-check passedResearch & Science

Install Alphafold DB

skills CLI
$ npx skills add aipoch/medical-research-skills --skill alphafold-db -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install aipoch/medical-research-skills alphafold-db --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Evidence Insight/alphafold-db' .claude/skills/alphafold-db && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
alphafold-db
GitHub stars
2k
Token cost
~606 tokens
SKILL.md length
226 words
Files
7 (incl. scripts, references)
Skills in repo
567
Repo updated
First seen
Licence
MIT

At a glance

Access over 200M protein structures from AlphaFold DB; use when you need to retrieve predicted 3D structures (PDB/mmCIF), confidence metrics (pLDDT/PAE), or protein metadata by UniProt accession.

  • You need to retrieve predicted 3D structures (PDB/mmCIF)
  • SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 1 more section
  • Runs Python scripts from its folder; calls python
  • Confidence metrics (pLDDT/PAE)

What it does

Alphafold DB is an agent skill from aipoch/medical-research-skills. Access over 200M protein structures from AlphaFold DB; use when you need to retrieve predicted 3D structures (PDB/mmCIF), confidence metrics (pLDDT/PAE), or protein metadata by UniProt accession.

Its SKILL.md is about 610 tokens, which your agent loads only when the skill is triggered. The skill folder holds 9 other files, including scripts and reference files (for example `alphafold-db_audit_result_v1.json`, `out/P00520_metadata.json` and `references/api_reference.md`).

It sits in Research & Science, covering Protein structure and design. It works with AlphaFold and UniProt. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

  • You need to retrieve predicted 3D structures (PDB/mmCIF)
  • Confidence metrics (pLDDT/PAE)
  • Protein metadata by UniProt accession

Example prompts

  • “/alphafold-db”

Requirements

  • Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 1 file in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Alphafold DB loads about 606 tokens when it runs, and up to ~968 if it reads all its reference files. Until then it costs about 52 tokens; SKILL.md has 226 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~52
When it runs · the whole SKILL.md, loaded when a task matches
~606
With references · SKILL.md plus every file in references/, read only if the agent opens them
~968

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 226 words, ~606 tokens.

Download SKILL.mdSave it as .claude/skills/alphafold-db/SKILL.md (or your agent's skills folder). This skill also uses 6 other files; get the full folder from GitHub.
name
alphafold-db
description
Access over 200M protein structures from AlphaFold DB; use when you need to retrieve predicted 3D structures (PDB/mmCIF), confidence metrics (pLDDT/PAE), or protein metadata by UniProt accession.
license
MIT
author
AIPOCH

Source: https://github.com/aipoch/medical-research-skills

AlphaFold Database Skill

When to Use

  • You have a UniProt accession (e.g., P00520) and need to download its AlphaFold-predicted 3D structure in mmCIF or PDB format.
  • You want to assess prediction reliability using per-residue pLDDT confidence scores.
  • You need PAE (Predicted Aligned Error) data to support domain-level interpretation or inter-domain confidence checks.
  • You want to programmatically retrieve AlphaFold DB metadata (e.g., model/structure URLs and related fields) for downstream pipelines.
  • You are building an automated workflow that fetches structures + confidence metrics for many proteins by UniProt ID.

Key Features

  • Fetch AlphaFold DB predicted structures by UniProt accession.
  • Download structure files in mmCIF (default) or PDB.
  • Retrieve and save metadata JSON, including confidence-related fields (e.g., pLDDT) and URL information.
  • Simple CLI workflow suitable for scripting and batch processing.

Dependencies

  • Python >=3.8
  • requests >=2.25

Example Usage

Fetch the structure and metadata for a UniProt ID and save them to a directory:

bash
python scripts/fetch_structure.py --uniprot_id P00520 --output_dir ./out --format cif

Fetch as PDB instead:

bash
python scripts/fetch_structure.py --uniprot_id P00520 --output_dir ./out --format pdb

Expected outputs in ./out:

  • P00520.cif (or P00520.pdb)
  • P00520_metadata.json (includes confidence/URL fields such as pLDDT-related information)

Implementation Details

  • Input identifier: UniProt accession ID (e.g., P00520).
  • Formats:
    • --format cif (default): downloads an mmCIF structure file.
    • --format pdb: downloads a PDB structure file.
  • Artifacts written:
    • Structure file named <UNIPROT_ID>.<cif|pdb>.
    • Metadata JSON named <UNIPROT_ID>_metadata.json, used to store confidence metrics (e.g., pLDDT) and AlphaFold DB URL-related fields.
  • API reference: Endpoint and response details are documented in references/api_reference.md.

© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 6 other files (scripts, references) in scientific-skills/Evidence Insight/alphafold-db of aipoch/medical-research-skills.

  • SKILL.md
  • alphafold-db_audit_result_v1.json
  • out/P00520.cif
  • out/P00520.pdb
  • out/P00520_metadata.json
  • references/api_reference.md
  • scripts/fetch_structure.py

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Alphafold DB next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Alphafold DB compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Alphafold DB this skillaipoch/medical-research-skills2k—~606Automated safety check: PassMIT
Alphafold Database Fetch And Analyzegoogle-deepmind/science-skills3.2k2 repos~1.2kAutomated safety check: PassApache-2.0
Bio DB ToolsDrugClaw/DrugClaw125—~1.4kAutomated safety check: PassApache-2.0
Ggetdavila7/claude-code-templates32k11 repos~6.3kAutomated safety check: PassMIT
Alphafold Databasedavila7/claude-code-templates32k10 repos~4kAutomated safety check: PassMIT
Foldseek Structural Searchgoogle-deepmind/science-skills3.2k1 repos~1.3kAutomated safety check: PassApache-2.0

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Works with

Categories

Questions about Alphafold DB

What does Alphafold DB do?

Access over 200M protein structures from AlphaFold DB; use when you need to retrieve predicted 3D structures (PDB/mmCIF), confidence metrics (pLDDT/PAE), or protein metadata by UniProt accession. Alphafold DB is an agent skill from aipoch/medical-research-skills. Access over 200M protein structures from AlphaFold DB; use when you need to retrieve predicted 3D structures (PDB/mmCIF), confidence metrics (pLDDT/PAE), or protein metadata by UniProt accession.

When should I use Alphafold DB?

Alphafold DB fits situations like: you need to retrieve predicted 3D structures (PDB/mmCIF); confidence metrics (pLDDT/PAE); protein metadata by UniProt accession.

How do I install Alphafold DB in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill alphafold-db -a claude-code`. Or copy the skill folder (scientific-skills/Evidence Insight/alphafold-db in aipoch/medical-research-skills) into .claude/skills/alphafold-db in your project. Claude Code loads it when a task matches its description.

How do I install Alphafold DB in Codex?

Run `npx skills add aipoch/medical-research-skills --skill alphafold-db -a codex`. Or copy the skill folder (scientific-skills/Evidence Insight/alphafold-db in aipoch/medical-research-skills) into .agents/skills/alphafold-db in your project. Codex loads it when a task matches its description.

Can I use Alphafold DB in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill alphafold-db -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/alphafold-db, .gemini/skills/alphafold-db, .github/skills/alphafold-db and .opencode/skills/alphafold-db in your project.

What does Alphafold DB need to run?

Going by SKILL.md and its folder, Alphafold DB needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Alphafold DB access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Alphafold DB safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Alphafold DB use?

Alphafold DB is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Alphafold DB use?

About 606 tokens (SKILL.md is roughly 2.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 362 tokens, read only when the agent opens those files.

What are the alternatives to Alphafold DB?

Skills that share tags, products or a category with Alphafold DB: Alphafold Database Fetch And Analyze (google-deepmind/science-skills, 3.2k stars), Bio DB Tools (DrugClaw/DrugClaw, 125 stars), Gget (davila7/claude-code-templates, 32k stars) and Alphafold Database (davila7/claude-code-templates, 32k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Alphafold DB?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,974 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.