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bindingdb-database

Query BindingDB for drug-target binding affinities by UniProt ID, compound name, or SMILES.

Updated Mar 10, 2026
Search Tags:#drug discovery#cheminformatics#protein-ligand#pharmacology#bindingdb#target affinity
One-click install
npx skills add https://github.com/Yezez9/Research-Agent --skill bindingdb-database
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bindingdb-database
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/bindingdb-database
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill bindingdb-database

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill provides access to BindingDB, a comprehensive resource for measured drug-target binding affinities, enabling researchers to quickly find and analyze interactions crucial for drug discovery and development.

Core Features & Use Cases

  • Query by Target: Find ligands that bind to a specific protein target using its UniProt ID.
  • Query by Compound: Search for binding data associated with a particular compound using its name or SMILES string.
  • Data Download & Analysis: Facilitates downloading and processing of the entire BindingDB dataset for large-scale analyses like SAR and polypharmacology profiling.
  • Use Case: A medicinal chemist needs to identify known inhibitors for a novel kinase target. They can use this Skill to query BindingDB by the target's UniProt ID and retrieve a list of compounds with their measured Ki or IC50 values.

Quick Start

Use the bindingdb-database skill to find all ligands with a Ki less than 100 nM for the UniProt target P00519.

Frequently Asked Questions about bindingdb-database

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

FAQPage Schema
How do I find drug-target binding affinities using a UniProt ID?▼

To find drug-target binding affinities, query the BindingDB database by entering a valid UniProt ID. This retrieves a list of associated ligands along with their measured Ki, Kd, IC50, or EC50 values.

Can I search BindingDB for protein-ligand interactions using a SMILES string?▼

Yes, you can search BindingDB for protein-ligand interactions using a compound name or a SMILES string. This returns available binding affinity data, including Ki and IC50 measurements, for the specified compound.

What measured binding affinity values can I retrieve for drug discovery?▼

You can retrieve Ki, Kd, IC50, and EC50 values from the BindingDB database for drug discovery. These measured drug-target binding affinities are essential for lead optimization and structure-activity relationship studies.

Does this Skill support bulk download of pharmacology data for polypharmacology profiling?▼

Yes, this Skill facilitates downloading and processing the entire BindingDB dataset for bulk pharmacology data analysis. This enables large-scale tasks like polypharmacology profiling and structure-activity relationship studies.

What is the best way to identify known inhibitors for a kinase target?▼

The best way to identify known inhibitors for a kinase target is querying BindingDB by the target's UniProt ID. This returns compounds with measured Ki or IC50 values, aiding lead optimization in drug discovery.

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