# Bindingdb Database

> BindingDB Database Skill Summary

- Skill: `lamm-mit/bindingdb-database` (Agent Skill)
- Install (CLI): `npx skillmds@latest add lamm-mit/bindingdb-database`
- Raw SKILL.md: https://api.skillmd.com/api/skills/lamm-mit/bindingdb-database/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: lamm-mit (https://skillmd.com/u/lamm-mit)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/lamm-mit/bindingdb-database

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# BindingDB Database Skill Summary

## Overview
BindingDB is a major public repository containing "over 3 million binding data records for ~1.4 million compounds tested against ~9,200 protein targets." The database stores quantitative binding measurements essential for pharmaceutical research and computational chemistry.

## Primary Use Cases
This resource excels when researchers need to:
- Identify known compounds that bind to specific protein targets
- Conduct structure-activity relationship (SAR) analyses examining how molecular modifications impact binding strength
- Assess compound selectivity across multiple protein targets
- Source curated affinity datasets for machine learning applications
- Evaluate potential off-target binding for drug repurposing studies

## Core Query Methods
The skill provides multiple access approaches: REST API queries by UniProt target ID, compound name searches, SMILES-based lookups, and large-scale TSV file downloads for comprehensive analysis.

## Key Measurement Types
BindingDB tracks four primary affinity metrics: Ki (inhibition constant), Kd (dissociation constant), IC50 (half-maximal inhibition), and EC50 (half-maximal effectiveness). Values below 10 nM typically indicate drug-potency compounds.

## Data Quality Considerations
Results should be filtered by target organism to ensure human protein relevance, and users should recognize that IC50 values vary based on experimental conditions like substrate concentration.