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bindingdb-database

Retrieve BindingDB affinities for proteins and ligands by UniProt IDs, SMILES, or PubChem IDs.

1|Updated Mar 11, 2026
Search Tags:#bioinformatics#drug-discovery#smiles#uniprot#sar#bindingdb#binding-affinity
One-click install
npx skills add https://github.com/SciMate-AI/scicli --skill bindingdb-database-scimate-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bindingdb-database
Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/bindingdb-database
Command: npx skills add https://github.com/SciMate-AI/scicli --skill bindingdb-database-scimate-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

BindingDB provides a public resource of experimentally measured binding affinities for protein targets and chemical ligands, enabling programmatic access to retrieve Ki, Kd, IC50, and EC50 data.

Core Features & Use Cases

  • Programmatic querying of BindingDB by target (UniProt) or compound (SMILES/name)
  • Retrieve multiple affinity metrics (Ki, Kd, IC50, EC50) for SAR and lead optimization
  • Use cases include target-focused inhibitor discovery, selectivity profiling, and cross-target data gathering for ML datasets

Quick Start

Query BindingDB for Ki data for UniProt ID P00519.

Frequently Asked Questions about bindingdb-database

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

FAQPage Schema
How do I retrieve binding affinity data like Ki and IC50 for a specific protein target?▼

Retrieve binding affinities by querying the BindingDB API with a UniProt ID. This returns experimentally measured Ki, Kd, IC50, and EC50 values for ligands associated with that protein target.

What is the best way to find compound binding data using SMILES strings or PubChem IDs?▼

Use the BindingDB getAffinitiesByCompoundName endpoint to query by compound SMILES or PubChem IDs. This retrieves target binding affinities to support drug discovery and selectivity profiling.

Can I gather cross-target binding affinity datasets for machine learning models?▼

Yes, you can programmatically query BindingDB to gather cross-target binding affinity datasets. Retrieving Ki, Kd, IC50, and EC50 data across multiple targets provides labeled examples for training ML models.

Does querying BindingDB require internet access to external REST APIs?▼

Yes, retrieving binding data requires internet access to the BindingDB REST API. The workflow queries live endpoints such as getLigandsByUniprotID and getAffinitiesByCompoundName to fetch affinity metrics.

How do I assess ligand selectivity across multiple protein targets during lead optimization?▼

Retrieve binding affinities for a ligand across multiple protein targets using BindingDB. Comparing Ki or IC50 values enables selectivity profiling to identify potent and selective compounds for lead optimization.

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