Agent skill

Pdb Database

by aipoch in aipoch/medical-research-skills

Access the RCSB Protein Data Bank (PDB) to search, download, and programmatically retrieve 3D macromolecular structures and metadata; use when you need structure discovery (text/sequence/3D…

MITAuto-check passedResearch & Science

Install Pdb Database

skills CLI

$ npx skills add aipoch/medical-research-skills --skill pdb-database -a claude-code

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

GitHub CLI

$ gh skill install aipoch/medical-research-skills pdb-database --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/pdb-database' .claude/skills/pdb-database && 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/

Paste into Claude Code

Install the "pdb-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/pdb-database into .claude/skills/pdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdb-database", then confirm the skill loads.

Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

$skill-installer

$skill-installer install https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/pdb-database

Type this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill pdb-database -a codex

Project install goes to .agents/skills/; add -g for ~/.codex/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills pdb-database --agent codex

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/'scientific-skills/Evidence Insight/pdb-database' .agents/skills/pdb-database && rm -rf skills-src

Use ~/.agents/skills/ instead of .agents/skills for a personal install.

Codex skills documentation · loads skills from .agents/skills/

Paste into Codex

Install the "pdb-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/pdb-database into .agents/skills/pdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdb-database", then confirm the skill loads.

Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill pdb-database -a cursor

Project install goes to .agents/skills/; add -g for ~/.cursor/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills pdb-database --agent cursor

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/'scientific-skills/Evidence Insight/pdb-database' .cursor/skills/pdb-database && rm -rf skills-src

Use ~/.cursor/skills/ instead of .cursor/skills for a personal install.

Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/

Paste into Cursor

Install the "pdb-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/pdb-database into .cursor/skills/pdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdb-database", then confirm the skill loads.

Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

gemini skills install

$ gemini skills install https://github.com/aipoch/medical-research-skills.git --path 'scientific-skills/Evidence Insight/pdb-database'

--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill pdb-database -a gemini-cli

Project install goes to .agents/skills/; add -g for ~/.gemini/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills pdb-database --agent gemini-cli

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/'scientific-skills/Evidence Insight/pdb-database' .gemini/skills/pdb-database && rm -rf skills-src

Use ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.

Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/

Paste into Gemini CLI

Install the "pdb-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/pdb-database into .gemini/skills/pdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdb-database", then confirm the skill loads.

Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

GitHub CLI

$ gh skill install aipoch/medical-research-skills pdb-database

Installs for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).

skills CLI

$ npx skills add aipoch/medical-research-skills --skill pdb-database -a github-copilot

Project install goes to .agents/skills/; add -g for ~/.copilot/skills/.

Manual copy

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

Use ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.

GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/

Paste into GitHub Copilot

Install the "pdb-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/pdb-database into .github/skills/pdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdb-database", then confirm the skill loads.

GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

skills CLI

$ npx skills add aipoch/medical-research-skills --skill pdb-database -a opencode

OpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.

GitHub CLI

$ gh skill install aipoch/medical-research-skills pdb-database --agent opencode

Project scope by default (.agents/skills/); add --scope user for a personal install.

Manual copy

$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/'scientific-skills/Evidence Insight/pdb-database' .opencode/skills/pdb-database && rm -rf skills-src

Use ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.

OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/

Paste into OpenCode

Install the "pdb-database" agent skill from https://github.com/aipoch/medical-research-skills/tree/main/scientific-skills/Evidence%20Insight/pdb-database into .opencode/skills/pdb-database/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "pdb-database", then confirm the skill loads.

OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.

Facts

Skill name: pdb-database
GitHub stars: 2k
Token cost: ~1.6k tokens
SKILL.md length: 374 words
Files: 3 (incl. references)
Skills in repo: 567
Repo updated: Sep 17, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Access the RCSB Protein Data Bank (PDB) to search, download, and programmatically retrieve 3D macromolecular structures and metadata; use when you need structure discovery (text/sequence/3D…

You need structure discovery (text/sequence/3D similarity)
SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 1 more section
Calls uv; reaches files.rcsb.org
Automated structural data ingestion for structural biology and drug discovery workflows

What it does

Pdb Database is an agent skill from aipoch/medical-research-skills. Access the RCSB Protein Data Bank (PDB) to search, download, and programmatically retrieve 3D macromolecular structures and metadata; use when you need structure discovery (text/sequence/3D similarity) or automated structural data ingestion for structural biology and drug discovery workflows.

Its SKILL.md is about 1.6k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files, including reference files (for example `pdb-database_audit_result_v1.json` and `references/api_reference.md`).

It sits in Research & Science, covering Data pipelines and ETL, Protein structure and design and Drug discovery and cheminformatics. 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 structure discovery (text/sequence/3D similarity)
Automated structural data ingestion for structural biology and drug discovery workflows

Example prompts

“/pdb-database”

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
Shell commands in SKILL.md call:
- uv
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:
- files.rcsb.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 Database loads about 1.6k tokens when it runs, and up to ~5.6k if it reads all its reference files. Until then it costs about 77 tokens; SKILL.md has 374 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~77
When it runs · the whole SKILL.md, loaded when a task matches: ~1.6k
With references · SKILL.md plus every file in references/, read only if the agent opens them: ~5.6k

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 aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 374 words, ~1,561 tokens.

Download SKILL.mdSave it as .claude/skills/pdb-database/SKILL.md (or your agent's skills folder). This skill also uses 2 other files; get the full folder from GitHub.

name: pdb-database
description: Access the RCSB Protein Data Bank (PDB) to search, download, and programmatically retrieve 3D macromolecular structures and metadata; use when you need structure discovery (text/sequence/3D similarity) or automated structural data ingestion for structural biology and drug discovery workflows.
license: MIT
author: AIPOCH

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

When to Use

Use this skill when you need to:

Find protein/nucleic acid 3D structures by keywords, organism, experimental method, or resolution.
Identify related structures via sequence similarity (e.g., homolog search for modeling).
Identify related structures via 3D structure similarity (e.g., fold-level comparisons).
Download coordinates (PDB/mmCIF) for downstream analysis, visualization, docking, or modeling.
Run batch retrieval of metadata/coordinates to feed pipelines in drug discovery, protein engineering, or structural bioinformatics.

Key Features

Text and attribute-based search over RCSB PDB entries.
Sequence similarity search with configurable thresholds (e-value, identity).
Structure similarity search using an existing entry as a query.
Programmatic metadata retrieval via the RCSB Data API (schema-based or GraphQL).
Direct coordinate downloads in PDB and mmCIF formats.
Batch processing patterns for multiple PDB IDs.

Dependencies

rcsb-api (latest recommended; provides rcsbapi.search and rcsbapi.data)
requests>=2.0 (HTTP downloads)
biopython>=1.80 (optional; parsing/analyzing PDB coordinates)

Install (example):

bash

uv pip install rcsb-api requests biopython

Example Usage

The following script is end-to-end runnable: it searches for a target, fetches metadata, downloads coordinates, and parses the structure.

python

#!/usr/bin/env python3
import pathlib
import requests

from rcsbapi.search import TextQuery, AttributeQuery
from rcsbapi.search.attrs import rcsb_entry_info
from rcsbapi.data import fetch, Schema

from Bio.PDB import PDBParser


def download_text(url: str, out_path: pathlib.Path) -> None:
    r = requests.get(url, timeout=60)
    r.raise_for_status()
    out_path.write_text(r.text, encoding="utf-8")


def main():
    out_dir = pathlib.Path("pdb_out")
    out_dir.mkdir(exist_ok=True)

    # 1) Search: hemoglobin entries with resolution < 2.0 Å
    q_text = TextQuery("hemoglobin")
    q_res = AttributeQuery(
        attribute=rcsb_entry_info.resolution_combined,
        operator="less",
        value=2.0,
    )
    query = q_text & q_res

    pdb_ids = list(query())[:5]
    if not pdb_ids:
        raise SystemExit("No results found.")
    pdb_id = pdb_ids[0]
    print(f"Selected PDB ID: {pdb_id}")

    # 2) Fetch entry metadata
    entry = fetch(pdb_id, schema=Schema.ENTRY)
    title = entry.get("struct", {}).get("title")
    method = (entry.get("exptl") or [{}])[0].get("method")
    resolution = (entry.get("rcsb_entry_info") or {}).get("resolution_combined")
    deposit_date = (entry.get("rcsb_accession_info") or {}).get("deposit_date")

    print("Metadata:")
    print(f"  Title: {title}")
    print(f"  Method: {method}")
    print(f"  Resolution: {resolution}")
    print(f"  Deposit date: {deposit_date}")

    # 3) Download coordinates (PDB and mmCIF)
    pdb_path = out_dir / f"{pdb_id}.pdb"
    cif_path = out_dir / f"{pdb_id}.cif"

    download_text(f"https://files.rcsb.org/download/{pdb_id}.pdb", pdb_path)
    download_text(f"https://files.rcsb.org/download/{pdb_id}.cif", cif_path)
    print(f"Downloaded: {pdb_path} and {cif_path}")

    # 4) Parse PDB coordinates (example: count atoms)
    parser = PDBParser(QUIET=True)
    structure = parser.get_structure(pdb_id, str(pdb_path))

    atom_count = sum(1 for _ in structure.get_atoms())
    chain_ids = sorted({chain.id for chain in structure.get_chains()})
    print("Parsed structure:")
    print(f"  Chains: {chain_ids}")
    print(f"  Atom count: {atom_count}")


if __name__ == "__main__":
    main()

Implementation Details

Search Modes and Query Composition

Text search uses free-text matching over entry annotations (titles, keywords, descriptions).
Attribute search filters by structured fields (e.g., organism, method, resolution).
Sequence similarity search typically supports:
- evalue_cutoff: lower is more stringent (fewer, more confident hits).
- identity_cutoff: fraction identity threshold (e.g., 0.9 for near-identical).
Structure similarity search uses an existing structure (e.g., an entry_id) as the geometric reference.
Queries can be combined with boolean logic:
- query1 & query2 (AND)
- query1 | query2 (OR)
- ~query (NOT), where supported by the client

Show full SKILL.md (126 more words)Show less

Data Retrieval (Schema vs GraphQL)

Schema-based fetch (e.g., Schema.ENTRY, Schema.POLYMER_ENTITY) is convenient for common objects and stable access patterns.
GraphQL fetch is best when you need a custom selection of fields in one request (reduce round-trips and payload).

Example GraphQL pattern:

python

from rcsbapi.data import fetch

query = """
{
  entry(entry_id: "4HHB") {
    struct { title }
    exptl { method }
    rcsb_entry_info { resolution_combined deposited_atom_count }
  }
}
"""
data = fetch(query_type="graphql", query=query)

Coordinate Downloads and Formats

PDB: legacy text format; widely supported but less expressive for large/complex structures.
mmCIF (PDBx): modern standard; preferred for completeness and large structures.

Direct download endpoints:

https://files.rcsb.org/download/{PDB_ID}.pdb
https://files.rcsb.org/download/{PDB_ID}.cif

Batch Processing Pattern

For batch metadata retrieval, iterate over IDs and call fetch(pdb_id, schema=Schema.ENTRY); handle exceptions per-ID to keep pipelines robust. For large batches, consider rate limiting and caching to avoid repeated downloads.

Reference Documentation

If present in this repository, consult:

references/api_reference.md for advanced endpoint usage, query patterns, schema notes, rate limits, and troubleshooting.

Files

SKILL.md and 2 other files (references) in scientific-skills/Evidence Insight/pdb-database of aipoch/medical-research-skills.

SKILL.md
pdb-database_audit_result_v1.json
references/api_reference.md

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Pdb Database 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 Database compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Pdb Database this skillaipoch/medical-research-skills	2k	—	~1.6k	Automated safety check: Pass	MIT	20 days ago
DiffDock Molecular DockingK-Dense-AI/scientific-agent-skills	48k	1 repos	~3k	Automated safety check: Notes	MIT	2 days ago
Biopipelineslocbp-uzh/biopipelines	109	—	~2.4k	Automated safety check: Pass	MIT	7 days ago
Tooluniverseynulihao/AgentSkillOS	617	3 repos	~2.5k	Automated safety check: Pass	None	7 mo ago
Pdb Databasedavila7/claude-code-templates	32k	9 repos	~2.3k	Automated safety check: Pass	MIT	yesterday
Chai1JimLiu/science-skills	227	4 repos	~1.2k	Automated safety check: Pass	Apache-2.0	3 mo ago

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Questions about Pdb Database

What does Pdb Database do?

Access the RCSB Protein Data Bank (PDB) to search, download, and programmatically retrieve 3D macromolecular structures and metadata; use when you need structure discovery (text/sequence/3D…. Pdb Database is an agent skill from aipoch/medical-research-skills. Access the RCSB Protein Data Bank (PDB) to search, download, and programmatically retrieve 3D macromolecular structures and metadata; use when you need structure discovery (text/sequence/3D similarity) or automated structural data ingestion for structural biology and drug discovery workflows.

When should I use Pdb Database?

Pdb Database fits situations like: you need structure discovery (text/sequence/3D similarity); automated structural data ingestion for structural biology and drug discovery workflows.

How do I install Pdb Database in Claude Code?

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

How do I install Pdb Database in Codex?

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

Can I use Pdb Database 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 pdb-database -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-database, .gemini/skills/pdb-database, .github/skills/pdb-database and .opencode/skills/pdb-database in your project.

What does Pdb Database need to run?

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

Does Pdb Database access the network?

SKILL.md names 1 domain. In commands or code: files.rcsb.org; the agent is likely to contact it when it follows the instructions. This is read from the text; nothing was executed.

Is Pdb Database 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 Database use?

Pdb Database 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 Pdb Database use?

About 1.6k tokens (SKILL.md is roughly 6.2k 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 4k tokens, read only when the agent opens those files.

What are the alternatives to Pdb Database?

Skills that share tags, products or a category with Pdb Database: DiffDock Molecular Docking (K-Dense-AI/scientific-agent-skills, 48k stars), Biopipelines (locbp-uzh/biopipelines, 109 stars), Tooluniverse (ynulihao/AgentSkillOS, 617 stars) and Pdb 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 Pdb Database?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,973 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.

Install Pdb Database

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

When to Use

Key Features

Dependencies

Example Usage

Implementation Details

Search Modes and Query Composition

Data Retrieval (Schema vs GraphQL)

Coordinate Downloads and Formats

Batch Processing Pattern

Reference Documentation

Files

Compare with similar skills

Similar skills

More from aipoch/medical-research-skills

Related

Questions about Pdb Database