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Agent skill

Pdb Structure API

by wentorai in wentorai/research-plugins

Search and retrieve 3D protein structures from the RCSB Protein Data Bank

MITAuto-check passedResearch & Science

Install Pdb Structure API

skills CLI
$ npx skills add wentorai/research-plugins --skill pdb-structure-api -a claude-code

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

GitHub CLI
$ gh skill install wentorai/research-plugins pdb-structure-api --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/wentorai/research-plugins.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/domains/biomedical/pdb-structure-api .claude/skills/pdb-structure-api && 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
pdb-structure-api
GitHub stars
298
Used in
1 other repo
Token cost
~1.9k tokens
SKILL.md length
366 words
Files
1
Skills in repo
405
Repo updated
First seen
Licence
MIT

At a glance

Search and retrieve 3D protein structures from the RCSB Protein Data Bank

  • Tasks that involve Protein structure and design
  • SKILL.md covers Overview, Authentication, Core Endpoints and Rate Limits, plus 3 more sections
  • Calls curl; reaches data.rcsb.org and search.rcsb.org

What it does

Pdb Structure API is an agent skill from wentorai/research-plugins. Search and retrieve 3D protein structures from the RCSB Protein Data Bank

Its SKILL.md is about 1.9k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

It sits in Research & Science, covering Protein structure and design. The repository describes itself as: 350+ academic research skills, MCP configs, and plugins for Research-Claw and AI agents. The licence is MIT.

When your agent uses it

  • Tasks that involve Protein structure and design

Example prompts

  • “/pdb-structure-api”

Requirements

  • Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit bf44b3c. 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

    Shell commands in SKILL.md call:

    • curl

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

  • Network

    Hosts in commands or code, which the agent is likely to contact:

    • data.rcsb.org
    • search.rcsb.org
    • files.rcsb.org

    Also links to:

    • rcsb.org
    • wwpdb.org

    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

Pdb Structure API loads about 1.9k tokens when it runs. Until then it costs about 23 tokens; SKILL.md has 366 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~23
When it runs · the whole SKILL.md, loaded when a task matches
~1.9k

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); files beside SKILL.md are not scanned.

SKILL.md

The full file from wentorai/research-plugins at commit bf44b3c, republished under its MIT licence (© wentorai). 366 words, ~1,850 tokens.

Download SKILL.mdSave it as .claude/skills/pdb-structure-api/SKILL.md (or your agent's skills folder).
name
pdb-structure-api
description
Search and retrieve 3D protein structures from the RCSB Protein Data Bank

RCSB Protein Data Bank API Guide

Overview

The RCSB Protein Data Bank (PDB) is the single global archive for experimentally determined 3D structures of biological macromolecules. It hosts over 200,000 structures resolved by X-ray crystallography, cryo-EM, NMR spectroscopy, and other methods. Each entry includes atomic coordinates, experimental metadata, polymer sequences, bound ligands, and literature references.

Two complementary APIs are available. The Data API (data.rcsb.org) serves structured entry metadata, polymer entities, and chemical components via RESTful GET endpoints. The Search API (search.rcsb.org) supports full-text, attribute-based, sequence similarity, and structure similarity searches.

Authentication

No authentication required. Both APIs are freely accessible without API keys, tokens, or registration.

Core Endpoints

Data API: Get Entry by PDB ID

Retrieve metadata for a structure including experimental method, resolution, citations, and bound components.

  • URL: GET https://data.rcsb.org/rest/v1/core/entry/{pdb_id}
bash
curl "https://data.rcsb.org/rest/v1/core/entry/4HHB"
  • Response (key fields):
json
{
  "rcsb_id": "4HHB",
  "struct": {
    "title": "THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS RESOLUTION"
  },
  "exptl": [{"method": "X-RAY DIFFRACTION"}],
  "rcsb_entry_info": {
    "deposited_atom_count": 4779,
    "molecular_weight": 64.74,
    "polymer_composition": "heteromeric protein",
    "polymer_entity_count_protein": 2,
    "resolution_combined": [1.74],
    "nonpolymer_bound_components": ["HEM"]
  }
}
Data API: Get Polymer Entity

Retrieve protein/nucleic acid entity details including sequence, organism, and gene info.

  • URL: GET https://data.rcsb.org/rest/v1/core/polymer_entity/{pdb_id}/{entity_id}
bash
curl "https://data.rcsb.org/rest/v1/core/polymer_entity/4HHB/1"
  • Response (key fields):
json
{
  "entity_poly": {
    "pdbx_seq_one_letter_code_can": "VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH...",
    "rcsb_entity_polymer_type": "Protein",
    "rcsb_sample_sequence_length": 141,
    "type": "polypeptide(L)"
  },
  "entity_src_gen": [{
    "gene_src_common_name": "Human",
    "pdbx_gene_src_scientific_name": "Homo sapiens",
    "pdbx_gene_src_ncbi_taxonomy_id": "9606"
  }]
}
Data API: Get Chemical Component

Retrieve ligand or small molecule metadata by component ID.

  • URL: GET https://data.rcsb.org/rest/v1/core/chemcomp/{comp_id}
bash
curl "https://data.rcsb.org/rest/v1/core/chemcomp/HEM"
  • Response (key fields):
json
{
  "rcsb_id": "HEM",
  "chem_comp": {
    "formula": "C34 H32 Fe N4 O4",
    "formula_weight": 616.487,
    "name": "PROTOPORPHYRIN IX CONTAINING FE",
    "type": "non-polymer"
  }
}
Search API: Full-Text Search

Search across all PDB entries with free-text queries. Returns ranked results by relevance.

  • URL: POST https://search.rcsb.org/rcsbsearch/v2/query
  • Headers: Content-Type: application/json
  • Key body fields: query.type ("terminal"), query.service ("full_text", "text", "sequence", "structure"), query.parameters.value, return_type ("entry", "polymer_entity", "assembly"), request_options.paginate.start/rows
bash
curl -X POST "https://search.rcsb.org/rcsbsearch/v2/query" \
  -H "Content-Type: application/json" \
  -d '{
    "query": {
      "type": "terminal",
      "service": "full_text",
      "parameters": {"value": "hemoglobin"}
    },
    "return_type": "entry",
    "request_options": {
      "results_content_type": ["experimental"],
      "paginate": {"start": 0, "rows": 3}
    }
  }'
  • Response:
json
{
  "query_id": "6f7192a6-d65b-4ff1-9d94-37b9600a8864",
  "result_type": "entry",
  "total_count": 8960,
  "result_set": [
    {"identifier": "3GOU", "score": 1.0},
    {"identifier": "6IHX", "score": 0.9995},
    {"identifier": "2PGH", "score": 0.9985}
  ]
}

For attribute-based searches, use "service": "text" with "attribute" and "operator" fields. Combine multiple criteria with "type": "group" and "logical_operator": "and".

Show full SKILL.md (131 more words)Show less

Rate Limits

No formal rate limits or rate-limit headers are published. RCSB recommends reasonable request rates. For bulk data, use FTP downloads at https://files.rcsb.org/pub/pdb/ or ftp://ftp.wwpdb.org/pub/pdb/ instead of iterative API calls.

Academic Use Cases

  • Structure-Based Drug Design: Retrieve target protein structures with bound ligands to analyze binding pockets, then search for similar structures to identify drug scaffolds.
  • Comparative Structural Analysis: Search all structures of a protein family, compare resolution and methods, select the best template for homology modeling.
  • Protein Engineering: Retrieve wild-type structures and cross-reference with mutant entries to analyze how mutations affect fold stability and ligand interactions.

Code Examples

Search and Retrieve Structures
python
import requests

# Search for kinase inhibitor structures
search_body = {
    "query": {"type": "terminal", "service": "full_text",
              "parameters": {"value": "tyrosine kinase inhibitor"}},
    "return_type": "entry",
    "request_options": {"results_content_type": ["experimental"],
                        "paginate": {"start": 0, "rows": 5}}
}
results = requests.post("https://search.rcsb.org/rcsbsearch/v2/query",
                        json=search_body).json()
print(f"Total hits: {results['total_count']}")

# Retrieve metadata for each hit
for hit in results["result_set"]:
    pdb_id = hit["identifier"]
    entry = requests.get(
        f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}").json()
    info = entry["rcsb_entry_info"]
    print(f"{pdb_id}: {entry['struct']['title'][:80]}")
    print(f"  Resolution: {info.get('resolution_combined', ['N/A'])[0]} A, "
          f"Method: {info['experimental_method']}")
Extract Polymer Sequences
python
import requests

pdb_id = "4HHB"
entry = requests.get(
    f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}").json()

for eid in range(1, entry["rcsb_entry_info"]["polymer_entity_count"] + 1):
    entity = requests.get(
        f"https://data.rcsb.org/rest/v1/core/polymer_entity/{pdb_id}/{eid}"
    ).json()
    poly = entity["entity_poly"]
    src = entity.get("rcsb_entity_source_organism", [{}])[0]
    print(f"Entity {eid}: {poly['rcsb_entity_polymer_type']} "
          f"({src.get('ncbi_scientific_name', 'N/A')})")
    print(f"  {poly['rcsb_sample_sequence_length']} residues: "
          f"{poly['pdbx_seq_one_letter_code_can'][:50]}...")

References

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

Files

Just SKILL.md in skills/domains/biomedical/pdb-structure-api of wentorai/research-plugins.

Open the folder on GitHubat commit bf44b3c

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in wentorai/research-plugins, which our catalogue first saw on October 7, 2026.

Compare with similar skills

Pdb Structure API 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.

Pdb Structure API compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Pdb Structure API this skillwentorai/research-plugins2981 repos~1.9kAutomated safety check: PassMIT
Msa Structure Prediction PipelineNVIDIA/skills3.5k1 repos~1.6kAutomated safety check: NotesApache-2.0
Interpro Databasemajiayu000/claude-skill-registry6662 repos~2.7kAutomated safety check: PassCC0-1.0
Fda Databasejaechang-hits/SciAgent-Skills3701 repos~4.5kAutomated safety check: PassCC0-1.0
Dailymed Databasejaechang-hits/SciAgent-Skills3701 repos~6kAutomated safety check: PassCC0-1.0
Ddinter Databasejaechang-hits/SciAgent-Skills3701 repos~7.3kAutomated safety check: PassCC-BY-4.0

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Categories

Questions about Pdb Structure API

What does Pdb Structure API do?

Search and retrieve 3D protein structures from the RCSB Protein Data Bank. Pdb Structure API is an agent skill from wentorai/research-plugins.

When should I use Pdb Structure API?

Pdb Structure API fits situations like: tasks that involve Protein structure and design.

How do I install Pdb Structure API in Claude Code?

Run `npx skills add wentorai/research-plugins --skill pdb-structure-api -a claude-code`. Or copy the skill folder (skills/domains/biomedical/pdb-structure-api in wentorai/research-plugins) into .claude/skills/pdb-structure-api in your project. Claude Code loads it when a task matches its description.

How do I install Pdb Structure API in Codex?

Run `npx skills add wentorai/research-plugins --skill pdb-structure-api -a codex`. Or copy the skill folder (skills/domains/biomedical/pdb-structure-api in wentorai/research-plugins) into .agents/skills/pdb-structure-api in your project. Codex loads it when a task matches its description.

Can I use Pdb Structure API 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 wentorai/research-plugins --skill pdb-structure-api -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/pdb-structure-api, .gemini/skills/pdb-structure-api, .github/skills/pdb-structure-api and .opencode/skills/pdb-structure-api in your project.

What does Pdb Structure API need to run?

Going by SKILL.md and its folder, Pdb Structure API needs the command-line tools its instructions call (curl). Our summary lists: Python 3.

Does Pdb Structure API access the network?

SKILL.md names 5 domains. In commands or code: data.rcsb.org, search.rcsb.org and files.rcsb.org; the agent is likely to contact these when it follows the instructions. As links in the text: rcsb.org and wwpdb.org. This is read from the text; nothing was executed.

Is Pdb Structure API 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. Review the folder before installing.

What licence does Pdb Structure API use?

Pdb Structure API is published under the MIT licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Pdb Structure API use?

About 1.9k tokens (SKILL.md is roughly 7.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Pdb Structure API?

Skills that share tags, products or a category with Pdb Structure API: Msa Structure Prediction Pipeline (NVIDIA/skills, 3.5k stars), Interpro Database (majiayu000/claude-skill-registry, 666 stars), Fda Database (jaechang-hits/SciAgent-Skills, 370 stars) and Dailymed Database (jaechang-hits/SciAgent-Skills, 370 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Pdb Structure API?

wentorai (a GitHub user) maintains it in wentorai/research-plugins, which has 298 GitHub stars. The repository holds 405 skills in this directory. The repository was last updated on June 19, 2026.

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