bindingdb-query

Query BindingDB for protein–ligand affinities via UniProt, PDB, or SMILES inputs.

130|4|Updated Mar 13, 2026

Search Tags:#rest-api #pdb #smiles #uniprot #drug-target #bindingdb #binding-affinity

Ready to run

npx skills add https://github.com/QSong-github/DrugClaw --skill bindingdb-query

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: bindingdb-query
Source: https://github.com/QSong-github/DrugClaw/tree/main/skills/dti/bindingdb
Command: npx skills add https://github.com/QSong-github/DrugClaw --skill bindingdb-query

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Binding affinity data for protein-ligand pairs is scattered across multiple sources and formats; this skill centralizes access to experimentally measured constants (Ki, Kd, IC50, EC50) from BindingDB, enabling quick, evidence-grounded retrieval.

Core Features & Use Cases

Auto-detects input as UniProt IDs, PDB IDs, or SMILES strings and fetches corresponding binding data.
Returns structured affinity records including target names, affinity types and values, and source identifiers (PMID/DOI).
Supports both single-entity and batch queries to support discovery and validation workflows.
Use case: researchers can look up binding data for a drug and its protein targets to support mechanism-of-action analyses or bibliography curation.

Quick Start

Ask the skill for binding affinities of a drug by name, for example imatinib.

Frequently Asked Questions about bindingdb-query

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I query BindingDB for drug-target binding affinities using a UniProt ID?▼

To query BindingDB for binding affinities using a UniProt ID, you provide the identifier as input and the skill auto-detects it to retrieve structured protein-ligand affinity records. This returns experimentally measured constants like Ki, Kd, IC50, and EC50.

Can I retrieve IC50 and Kd values using a SMILES string?▼

Yes, you can retrieve IC50 and Kd values using a SMILES string. The skill auto-detects SMILES inputs to fetch corresponding binding data from BindingDB, returning structured affinity records with target names and source identifiers like PMID or DOI.

What binding affinity metrics are supported by the BindingDB REST API?▼

The BindingDB REST API supports retrieval of Ki, Kd, IC50, and EC50 affinity metrics. It returns these experimentally measured constants as a unified, structured set of affinity records with optional literature identifiers.

Does BindingDB query support PDB IDs for protein-ligand binding data?▼

Yes, BindingDB query supports PDB IDs for fetching protein-ligand binding data. The skill auto-detects PDB ID inputs to retrieve affinity records, providing target names, affinity values, and source citations for mechanism-of-action analyses.

How do I look up binding data for a specific drug and its protein targets?▼

To look up binding data for a specific drug and its protein targets, you query the skill by drug name, SMILES, or protein identifier. It retrieves binding affinities from BindingDB, supporting both single-entity and batch discovery workflows.

Are there limits on the number of binding affinity records returned per query?▼

Yes, the skill caps the number of binding affinity records returned per query to ensure readability. This prevents overly large result sets when fetching structured protein-ligand binding data from the BindingDB public REST API.