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bindingdb-database

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

Updated Mar 15, 2026
Search Tags:#drug discovery#medicinal chemistry#target identification#pharmacology#affinity#bindingdb
One-click install
npx skills add https://github.com/sagunkayastha/claude_skills_collection --skill bindingdb-database-sagunkayastha
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bindingdb-database
Source: https://github.com/sagunkayastha/claude_skills_collection/tree/main/scientific-databases/bindingdb-database
Command: npx skills add https://github.com/sagunkayastha/claude_skills_collection --skill bindingdb-database-sagunkayastha

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, pandas, numpy, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides access to a comprehensive database of 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 compounds that bind to a specific protein using its UniProt ID.
  • Query by Compound: Search for binding data based on a compound's name or SMILES string.
  • Data Download & Analysis: Load and analyze large datasets for Structure-Activity Relationship (SAR) studies and machine learning model preparation.
  • Use Case: A medicinal chemist needs to find known inhibitors for a specific cancer target (e.g., EGFR). They can use this Skill to query BindingDB by the EGFR UniProt ID and retrieve a ranked list of compounds with their measured binding affinities (Ki, IC50).

Quick Start

Use the bindingdb-database skill to find the top 20 inhibitors for the target with UniProt ID P00533 using IC50 as the affinity type.

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 for a specific protein?▼

You can find drug-target binding affinities by querying the database with a target's UniProt ID to retrieve measured interaction values like Ki, Kd, IC50, and EC50 for drug discovery.

Can I search for compound binding data using a SMILES string?▼

Yes, you can search for binding data by querying a compound's name or SMILES string to retrieve its measured binding affinities for polypharmacology analysis and SAR studies.

How do I download large datasets of binding affinities for machine learning?▼

You can download large datasets of binding affinities as TSV files, which facilitates loading data into pandas and numpy for Structure-Activity Relationship studies and machine learning model preparation.

What measured binding values are available when querying BindingDB?▼

Querying BindingDB provides measured drug-target binding affinity values including Ki, Kd, IC50, and EC50, which are crucial for lead optimization and pharmacological analysis.

Does this Skill support polypharmacology profiling and SAR analysis?▼

Yes, the Skill supports polypharmacology profiling and SAR analysis by providing functions to search via UniProt ID or compound name and download TSV files for large-scale data analysis.

What's the best way to retrieve ranked inhibitors for a cancer target like EGFR?▼

Query BindingDB using the target's UniProt ID and specify IC50 as the affinity type to retrieve a ranked list of measured compounds for targets like EGFR.

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