Agent skill

Pdb

3D protein structure search via RCSB PDB. An agent skill from lamm-mit/scienceclaw.

Apache-2.0Auto-check passedResearch & Science

Install Pdb

skills CLI

$ npx skills add lamm-mit/scienceclaw --skill pdb -a claude-code

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

GitHub CLI

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

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

GitHub CLI

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

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

GitHub CLI

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

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

GitHub CLI

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

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

Manual copy

$ git clone --depth 1 https://github.com/lamm-mit/scienceclaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/pdb .github/skills/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 "pdb" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/pdb into .github/skills/pdb/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "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 lamm-mit/scienceclaw --skill 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 lamm-mit/scienceclaw 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/lamm-mit/scienceclaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/pdb .opencode/skills/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 "pdb" agent skill from https://github.com/lamm-mit/scienceclaw/tree/main/skills/pdb into .opencode/skills/pdb/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "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: pdb
GitHub stars: 244
Token cost: ~737 tokens
SKILL.md length: 223 words
Files: 3 (incl. scripts)
Skills in repo: 85
Repo updated: Aug 21, 2026
First seen: Oct 7, 2026
Licence: Apache-2.0

At a glance

3D protein structure search via RCSB PDB. An agent skill from lamm-mit/scienceclaw.

Tasks that involve Protein structure and design
SKILL.md covers Usage, Parameters, Examples and Output Fields, plus 2 more sections
Runs Python scripts from its folder; calls python3

What it does

Pdb is an agent skill from lamm-mit/scienceclaw. 3D protein structure search via RCSB PDB. Input MUST be a protein/gene name (e.g. 'KRAS', 'EGFR', 'BTK') or a 4-character PDB ID (e.g. '6OIM'). Returns zero results for drug/chemistry phrases such as 'covalent inhibitors' or 'warhead selectivity'. Strip all drug qualifiers and pass only the target protein name or PDB ID.

Its SKILL.md is about 740 tokens, which your agent loads only when the skill is triggered. The skill folder holds 4 other files, including scripts (for example `scripts/pdb_search.py`).

It sits in Research & Science, covering Protein structure and design. The licence is Apache-2.0.

When your agent uses it

Tasks that involve Protein structure and design

Example prompts

“) or a 4-character PDB ID (e.g.”
“). Returns zero results for drug/chemistry phrases such as”
“warhead selectivity”
“/pdb”

Requirements

Python 3

What it can do on your machine

Read from SKILL.md and the folder at commit ab9aba1. 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 2 files in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
- python3
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

Pdb loads about 737 tokens when it runs. Until then it costs about 82 tokens; SKILL.md has 223 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it: ~82
When it runs · the whole SKILL.md, loaded when a task matches: ~737

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 lamm-mit/scienceclaw at commit ab9aba1, republished under its Apache-2.0 licence (© lamm-mit). 223 words, ~737 tokens.

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

name: pdb
description: 3D protein structure search via RCSB PDB. Input MUST be a protein/gene name (e.g. 'KRAS', 'EGFR', 'BTK') or a 4-character PDB ID (e.g. '6OIM'). Returns zero results for drug/chemistry phrases such as 'covalent inhibitors' or 'warhead selectivity'. Strip all drug qualifiers and pass only the target protein name or PDB ID.

PDB - Protein Data Bank

Search and fetch protein structures from the RCSB Protein Data Bank.

Usage

Search for structures:

bash

python3 {baseDir}/scripts/pdb_search.py --query "kinase human"

Get structure details:

bash

python3 {baseDir}/scripts/pdb_search.py --pdb-id 1ATP

Search by sequence:

bash

python3 {baseDir}/scripts/pdb_search.py --sequence "MTEYKLVVVGAGGVGKSALTIQLIQ" --identity 70

Parameters

Parameter	Description	Default
`--query`	Text search query	-
`--pdb-id`	Specific PDB ID to fetch	-
`--sequence`	Sequence for similarity search	-
`--identity`	Minimum sequence identity %	90
`--max-results`	Maximum results	10
`--format`	Output: summary, detailed, json	summary

Examples

bash

# Search for insulin structures
python3 {baseDir}/scripts/pdb_search.py --query "insulin"

# Get details for a specific structure
python3 {baseDir}/scripts/pdb_search.py --pdb-id 4HHB

# Find structures similar to a sequence
python3 {baseDir}/scripts/pdb_search.py --sequence "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH" --identity 50

# Get JSON output
python3 {baseDir}/scripts/pdb_search.py --query "p53 DNA binding" --format json

Output Fields

PDB ID - 4-character structure identifier
Title - Structure title
Resolution - X-ray resolution in Angstroms
Method - Experimental method (X-RAY, NMR, EM)
Release Date - When structure was released
Organism - Source organism
Chains - Polymer chains in structure

Query Limitations — Read Before Using

PDB stores experimentally determined 3D structures. Queries must target proteins or genes with known deposited structures. Abstract or chemistry-only queries return zero results.

❌ Fails	✅ Works
"BTK covalent inhibitor"	"BTK" or "Bruton tyrosine kinase"
"warhead optimization"	"1K2P" (direct PDB ID)
"ADMET prediction"	"EGFR kinase inhibitor complex"

Tips for avoiding zero results:

Use short protein names or gene names: "BTK", "p53", "EGFR"
Use a specific PDB ID (--pdb-id 3K54) when you already have one from UniProt cross-refs
If zero results, broaden the query — e.g., "kinase" instead of "covalent kinase inhibitor BTK"
Not all proteins have PDB entries; check UniProt cross-refs first

Notes

Uses RCSB PDB REST API (no authentication)
Structures include X-ray, NMR, and cryo-EM
Resolution shown for X-ray structures
Links provided to 3D viewers

Files

SKILL.md and 2 other files (scripts) in skills/pdb of lamm-mit/scienceclaw.

SKILL.md
scripts/__pycache__/pdb_search.cpython-313.pyc
scripts/pdb_search.py

Open the folder on GitHubat commit ab9aba1

Compare with similar skills

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.

Pdb compared with similar skills
Skill	Stars	Used in	Tokens	Auto-check	Licence	Repo updated
Pdb this skilllamm-mit/scienceclaw	244	—	~737	Automated safety check: Pass	Apache-2.0	1 mo ago
Alphafold Database Fetch And Analyzegoogle-deepmind/science-skills	3.2k	2 repos	~1.2k	Automated safety check: Pass	Apache-2.0	22 days ago
Alphafoldadaptyvbio/protein-design-skills	163	4 repos	~1.2k	Automated safety check: Pass	MIT	3 mo ago
Bindcraftadaptyvbio/protein-design-skills	163	4 repos	~1.3k	Automated safety check: Pass	MIT	3 mo ago
Pymol VisualizationChatMol/ChatMol	372	—	~1.2k	Automated safety check: Pass	MIT	6 mo ago
Complexa Binder DesignNVIDIA-BioNeMo/bionemo-agent-toolkit	478	—	~3.1k	Automated safety check: Notes	Apache-2.0	today

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Questions about Pdb

What does Pdb do?

3D protein structure search via RCSB PDB. An agent skill from lamm-mit/scienceclaw. Pdb is an agent skill from lamm-mit/scienceclaw. 3D protein structure search via RCSB PDB.

When should I use Pdb?

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

How do I install Pdb in Claude Code?

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

How do I install Pdb in Codex?

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

Can I use 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 lamm-mit/scienceclaw --skill 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/pdb, .gemini/skills/pdb, .github/skills/pdb and .opencode/skills/pdb in your project.

What does Pdb need to run?

Going by SKILL.md and its folder, Pdb needs Python for the scripts in its folder and the command-line tools its instructions call (python3). Our summary lists: Python 3.

Does Pdb 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 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 Pdb use?

Pdb is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Pdb use?

About 737 tokens (SKILL.md is roughly 2.9k 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?

Skills that share tags, products or a category with Pdb: Alphafold Database Fetch And Analyze (google-deepmind/science-skills, 3.2k stars), Alphafold (adaptyvbio/protein-design-skills, 163 stars), Bindcraft (adaptyvbio/protein-design-skills, 163 stars) and Pymol Visualization (ChatMol/ChatMol, 372 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Pdb?

lamm-mit (a GitHub user) maintains it in lamm-mit/scienceclaw, which has 244 GitHub stars. The repository holds 85 skills in this directory. The repository was last updated on August 21, 2026.

Source: lamm-mit/scienceclaw 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

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

PDB - Protein Data Bank

Usage

Search for structures:

Get structure details:

Search by sequence:

Parameters

Examples

Output Fields

Query Limitations — Read Before Using

Notes

Files

Compare with similar skills

Similar skills

More from lamm-mit/scienceclaw

Related

Questions about Pdb