qsong-github/drugclaw/bindingdb

Name: bindingdb
Author: qsong-github

Claude Code and agent skill by qsong-github/drugclaw

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Query the BindingDB drug-target binding affinity database. Use whenever the user asks about protein-ligand binding data, affinity measurements (Ki, IC50, Kd, EC50), or wants to look up binding partners for a UniProt ID, PDB ID, or compound SMILES string.

Install

npx vskill@latest install qsong-github/drugclaw/bindingdb

SKILL.md

BindingDB Query Skill

Search BindingDB binding affinity records by any entity. Auto-detects type by pattern:

Input Pattern	Detected As	Example	API Endpoint
`P35355`, `Q9Y233`	UniProt ID	`P00533` (EGFR)	`getLigandsByUniprots`
`1Q0L`, `3ANM`	PDB ID (4-char, digit-leading)	`1Q0L`	`getLigandsByPDBs`
contains `=()#[]@/\`	SMILES string	`CC(=O)Oc1ccccc1C(O)=O`	`getTargetByCompound`
fallback	treated as UniProt	—	`getLigandsByUniprots`

API

Function	Input	Returns
`search(entity, cutoff)`	single entity string	dict with `entity`, `type`, `hits`, `affinities`
`search_batch(entities, cutoff)`	list of entity strings	dict[str, search_result]
`summarize(result)`	search() output	compact multi-line text
`to_json(result)`	search() output	list[dict] of affinity records
`query_by_uniprot(ids, cutoff)`	UniProt ID(s), nM cutoff	list[dict]
`query_by_pdb(ids, cutoff, identity)`	PDB ID(s), nM cutoff, % identity	list[dict]
`query_by_smiles(smiles, cutoff)`	SMILES, similarity 0–1	list[dict]

Parameters

cutoff (int): affinity threshold in nM (default 10 000). Entries with IC50/Ki/Kd ≤ cutoff are returned.
identity (int, PDB only): sequence-identity cutoff in percent (default 92).
Results are capped at 50 per query for LLM readability.

Usage

See if __name__ == "__main__" block in 26_BindingDB.py for runnable examples covering: UniProt single query, PDB query, SMILES compound query, batch query, and JSON output.

Key Fields in Each Affinity Record

Field	Description
`query`	Target protein name
`monomerid`	BindingDB compound ID
`smile`	SMILES structure of ligand
`affinity_type`	Ki, IC50, Kd, or EC50
`affinity`	Value in nM
`pmid`	PubMed ID of source
`doi`	DOI of source publication

Data Source

Database: BindingDB (https://www.bindingdb.org/)
Size: 3.2M data points, 1.4M compounds, 11.4K targets
Access: Public REST API (JSON), no authentication required
Citation: BindingDB in 2024: a FAIR knowledgebase of protein-small molecule binding data. Nucleic Acids Research, 53(D1), D1633 (2025). DOI: 10.1093/nar/gkae1199

Security

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Source

SKILL.md in the repositoryCheckingskills/dti/bindingdb/SKILL.md

Popularity

Repository stars: 116
Repository forks: 3
7-day trend score: 24

Stars and forks are for the whole GitHub repository, not this skill alone. Not refreshed yet.

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