Agent skill

Drug DB Pdb

by learningmatter-mit in learningmatter-mit/AtomisticSkills

Search, filter, and retrieve macromolecular structures from the RCSB Protein Data Bank (PDB), including metadata, bound ligands, and optional coordinate/validation downloads.

MITAuto-check passedResearch & Science

Install Drug DB Pdb

skills CLI

$ npx skills add learningmatter-mit/AtomisticSkills --skill drug-db-pdb -a claude-code

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

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills drug-db-pdb --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/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/drug-db-pdb .claude/skills/drug-db-pdb && 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 "drug-db-pdb" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-db-pdb into .claude/skills/drug-db-pdb/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-db-pdb", 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/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-db-pdb

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 learningmatter-mit/AtomisticSkills --skill drug-db-pdb -a codex

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

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills drug-db-pdb --agent codex

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

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/drug-db-pdb .agents/skills/drug-db-pdb && 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 "drug-db-pdb" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-db-pdb into .agents/skills/drug-db-pdb/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-db-pdb", 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 learningmatter-mit/AtomisticSkills --skill drug-db-pdb -a cursor

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

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills drug-db-pdb --agent cursor

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

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/drug-db-pdb .cursor/skills/drug-db-pdb && 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 "drug-db-pdb" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-db-pdb into .cursor/skills/drug-db-pdb/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-db-pdb", 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/learningmatter-mit/AtomisticSkills.git --path skills/drug-db-pdb

--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 learningmatter-mit/AtomisticSkills --skill drug-db-pdb -a gemini-cli

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

GitHub CLI

$ gh skill install learningmatter-mit/AtomisticSkills drug-db-pdb --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/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/drug-db-pdb .gemini/skills/drug-db-pdb && 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 "drug-db-pdb" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-db-pdb into .gemini/skills/drug-db-pdb/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-db-pdb", 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 learningmatter-mit/AtomisticSkills drug-db-pdb

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 learningmatter-mit/AtomisticSkills --skill drug-db-pdb -a github-copilot

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

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/drug-db-pdb .github/skills/drug-db-pdb && 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 "drug-db-pdb" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-db-pdb into .github/skills/drug-db-pdb/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-db-pdb", 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 learningmatter-mit/AtomisticSkills --skill drug-db-pdb -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 learningmatter-mit/AtomisticSkills drug-db-pdb --agent opencode

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

Manual copy

$ git clone --depth 1 https://github.com/learningmatter-mit/AtomisticSkills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/drug-db-pdb .opencode/skills/drug-db-pdb && 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 "drug-db-pdb" agent skill from https://github.com/learningmatter-mit/AtomisticSkills/tree/main/skills/drug-db-pdb into .opencode/skills/drug-db-pdb/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "drug-db-pdb", 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: drug-db-pdb
GitHub stars: 176
Token cost: ~1.1k tokens
SKILL.md length: 315 words
Files: 5 (incl. scripts)
Skills in repo: 129
Repo updated: Oct 7, 2026
First seen: Oct 7, 2026
Licence: MIT

At a glance

Search, filter, and retrieve macromolecular structures from the RCSB Protein Data Bank (PDB), including metadata, bound ligands, and optional coordinate/validation downloads.

Works in 6 steps: (Recommended) Create a dedicated output… → Search by keyword (full-text) → Search with structure-quality filters… → …
Research & Science work in your project
SKILL.md covers Goal, Instructions, Examples and Constraints
Runs Python scripts from its folder

What it does

Drug DB Pdb is an agent skill from learningmatter-mit/AtomisticSkills. Search, filter, and retrieve macromolecular structures from the RCSB Protein Data Bank (PDB), including metadata, bound ligands, and optional coordinate/validation downloads.

Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including scripts (for example `examples/1hsg_entry.json`, `examples/README.md` and `examples/hiv1_protease_search.json`).

It sits in Research & Science. The repository describes itself as: Integrating AtomisticSkills into Agentic IDEs (Cursor, Claude Code, Codex, Google Antigravity, Hermes Agent, etc). The licence is MIT.

When your agent uses it

Research & Science work in your project

Example prompts

“/drug-db-pdb”

Requirements

Python 3

Workflow steps

6 steps, taken from the step headings in SKILL.md.

(Recommended) Create a dedicated output directory
Search by keyword (full-text)
Search with structure-quality filters (recommended for drug discovery)
Retrieve a specific PDB entry by ID
Download coordinate files (mmCIF recommended)
(Recommended) Download wwPDB validation report PDF

What it can do on your machine

Read from SKILL.md and the folder at commit 6257444. 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.
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
- github.com
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

Drug DB Pdb loads about 1.1k tokens when it runs. Until then it costs about 47 tokens; SKILL.md has 315 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~47
When it runs · the whole SKILL.md, loaded when a task matches: ~1.1k

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 learningmatter-mit/AtomisticSkills at commit 6257444, republished under its MIT licence (© learningmatter-mit). 315 words, ~1,088 tokens.

Download SKILL.mdSave it as .claude/skills/drug-db-pdb/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.

name: drug-db-pdb
description: Search, filter, and retrieve macromolecular structures from the RCSB Protein Data Bank (PDB), including metadata, bound ligands, and optional coordinate/validation downloads.
metadata.category: drug-discovery
metadata.venv: cpu

db-pdb

Goal

To programmatically discover and retrieve protein (and protein-ligand complex) structures from the RCSB Protein Data Bank (PDB) by combining the RCSB Search API (to find matching PDB IDs) with the RCSB Data API (to retrieve rich metadata and ligand information), and optionally downloading coordinate files (PDB/mmCIF) and wwPDB validation reports for downstream modeling.

Instructions

1. (Recommended) Create a dedicated output directory

Keep downloaded coordinates/JSON in a reproducible folder.

bash

mkdir -p research/db-pdb/ace2_example

2. Search by keyword (full-text)

Uses the RCSB Search API to return the top scoring PDB IDs for a query.

bash

${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/query_pdb.py \
  --search "kinase inhibitor" \
  --max_results 10 \
  --output research/db-pdb/kinase_results.json

3. Search with structure-quality filters (recommended for drug discovery)

For ligand modeling, you often want:

An experimental method like X-RAY DIFFRACTION (or high-resolution cryo-EM).
A resolution cutoff (e.g., <= 2.5 A for X-ray, context dependent).

bash

${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/query_pdb.py \
  --search "ACE2" \
  --organism "Homo sapiens" \
  --method "X-RAY DIFFRACTION" \
  --resolution 2.5 \
  --max_results 25 \
  --output research/db-pdb/ace2_xray_le2p5.json

4. Retrieve a specific PDB entry by ID

This pulls metadata via the Data API and (by default) also collects bound ligands by enumerating non-polymer entities.

bash

${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/query_pdb.py \
  --pdb_id 1HSG \
  --output research/db-pdb/1hsg_info.json

5. Download coordinate files (mmCIF recommended)

The PDB ecosystem's canonical archival format is PDBx/mmCIF (legacy PDB format can be unavailable or insufficient for very large structures).

bash

${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/query_pdb.py \
  --pdb_id 1HSG \
  --download mmcif \
  --download_dir research/db-pdb/structures \
  --output research/db-pdb/1hsg_with_file.json

6. (Recommended) Download wwPDB validation report PDF

Quality assessment for experimental structures is standardized via wwPDB validation reports; these are especially important for ligand-bound structures in drug discovery workflows.

bash

${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/query_pdb.py \
  --pdb_id 1HSG \
  --download_validation \
  --download_dir research/db-pdb/validation \
  --output research/db-pdb/1hsg_with_validation.json

Examples

Search HIV-1 protease entries, then fetch + download the best candidate:

bash

${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/query_pdb.py \
  --search "HIV-1 protease" \
  --method "X-RAY DIFFRACTION" \
  --resolution 2.0 \
  --max_results 10 \
  --output research/db-pdb/hiv1_protease_candidates.json

bash

${CLAUDE_SKILL_DIR}/../../venv/run cpu python ${CLAUDE_SKILL_DIR}/scripts/query_pdb.py \
  --pdb_id 1HSG \
  --download mmcif \
  --download_validation \
  --download_dir research/db-pdb/hiv1_protease_files \
  --output research/db-pdb/1hsg_full.json

Constraints

API Rate Limits: RCSB PDB APIs are rate-limited; the script implements a minimum inter-request interval and exponential backoff on HTTP 429.
Ligand metadata: "Ligands" here refer to non-polymer entities in the PDB hierarchy. The script enumerates non-polymer entity IDs from the entry container identifiers and queries each nonpolymer entity object.
File formats: Prefer mmCIF for robustness; legacy PDB may be incomplete or unavailable for some entries.
Quality selection: For drug discovery, do not select structures using resolution alone -- use wwPDB validation reports and ligand-quality metrics when available.
Environment: Requires the cpu environment.

Author: Matthew Cox Contact: GitHub @mcox3406

Files

SKILL.md and 4 other files (scripts) in skills/drug-db-pdb of learningmatter-mit/AtomisticSkills.

SKILL.md
examples/1hsg_entry.json
examples/README.md
examples/hiv1_protease_search.json
scripts/query_pdb.py

Open the folder on GitHubat commit 6257444

Compare with similar skills

Drug DB Pdb 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.

Drug DB Pdb compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Drug DB Pdb this skilllearningmatter-mit/AtomisticSkills	176	—	~1.1k	Automated safety check: Pass	MIT	today
Hypothesis Generationspacering-net/codeg	3.8k	15 repos	~3.6k	Automated safety check: Notes	MIT	today
GitHub Deep Researchbytedance/deer-flow	83k	5 repos	~1.3k	Automated safety check: Pass	MIT	today
Nature Paper CardYuan1z0825/nature-skills	46k	2 repos	~2.1k	Automated safety check: Pass	Apache-2.0	yesterday
Read arXiv Paperkarpathy/nanochat	58k	2 repos	~494	Automated safety check: Pass	MIT	1 mo ago
Content Research Writerweapp-tailwindcss/weapp-tailwindcss	1.9k	25 repos	~3.5k	Automated safety check: Pass	MIT	today

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Questions about Drug DB Pdb

What does Drug DB Pdb do?

Search, filter, and retrieve macromolecular structures from the RCSB Protein Data Bank (PDB), including metadata, bound ligands, and optional coordinate/validation downloads. Drug DB Pdb is an agent skill from learningmatter-mit/AtomisticSkills. Search, filter, and retrieve macromolecular structures from the RCSB Protein Data Bank (PDB), including metadata, bound ligands, and optional coordinate/validation downloads.

When should I use Drug DB Pdb?

Drug DB Pdb fits situations like: research & Science work in your project.

How do I install Drug DB Pdb in Claude Code?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill drug-db-pdb -a claude-code`. Or copy the skill folder (skills/drug-db-pdb in learningmatter-mit/AtomisticSkills) into .claude/skills/drug-db-pdb in your project. Claude Code loads it when a task matches its description.

How do I install Drug DB Pdb in Codex?

Run `npx skills add learningmatter-mit/AtomisticSkills --skill drug-db-pdb -a codex`. Or copy the skill folder (skills/drug-db-pdb in learningmatter-mit/AtomisticSkills) into .agents/skills/drug-db-pdb in your project. Codex loads it when a task matches its description.

Can I use Drug DB Pdb 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 learningmatter-mit/AtomisticSkills --skill drug-db-pdb -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/drug-db-pdb, .gemini/skills/drug-db-pdb, .github/skills/drug-db-pdb and .opencode/skills/drug-db-pdb in your project.

What does Drug DB Pdb need to run?

Going by SKILL.md and its folder, Drug DB Pdb needs Python for the scripts in its folder. Our summary lists: Python 3.

Does Drug DB Pdb access the network?

SKILL.md names 1 domain. As links in the text: github.com. This is read from the text; nothing was executed.

Is Drug DB Pdb 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 Drug DB Pdb use?

Drug DB Pdb 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 Drug DB Pdb use?

About 1.1k tokens (SKILL.md is roughly 4.4k 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 Drug DB Pdb?

Skills that share tags, products or a category with Drug DB Pdb: Hypothesis Generation (spacering-net/codeg, 3.8k stars), GitHub Deep Research (bytedance/deer-flow, 83k stars), Nature Paper Card (Yuan1z0825/nature-skills, 46k stars) and Read arXiv Paper (karpathy/nanochat, 58k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Drug DB Pdb?

learningmatter-mit (a GitHub organization) maintains it in learningmatter-mit/AtomisticSkills, which has 176 GitHub stars. The repository holds 129 skills in this directory. The repository was last updated on October 7, 2026.

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

Install Drug DB Pdb

Facts

At a glance

What it does

When your agent uses it

Example prompts

Requirements

Workflow steps

What it can do on your machine

Tool permissions

Runs code

Network

Credentials

Context cost

Safety

SKILL.md

db-pdb

Goal

Instructions

1. (Recommended) Create a dedicated output directory

2. Search by keyword (full-text)

3. Search with structure-quality filters (recommended for drug discovery)

4. Retrieve a specific PDB entry by ID

5. Download coordinate files (mmCIF recommended)

6. (Recommended) Download wwPDB validation report PDF

Examples

Constraints

Files

Compare with similar skills

Similar skills

More from learningmatter-mit/AtomisticSkills

Related

Questions about Drug DB Pdb