# Bindingdb Database

Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50).

- Repository: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills (3090 stars)
- Category: Engineering
- License: CC-BY-3.0
- Last updated: 2026-07-21
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bindingdb-database -g -a claude-code -y`
Codex: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bindingdb-database -g -a codex -y`
Cursor: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bindingdb-database -g -a cursor -y`
Gemini CLI: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bindingdb-database -g -a gemini-cli -y`

## Description

Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathogen. Essential for drug discovery, lead optimization, polypharmacology analysis, and structure-activity relationship (SAR) studies.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# BindingDB Database

## Overview

BindingDB (https://www.bindingdb.org/) is the primary public database of measured drug-protein binding affinities. It contains over 3 million binding data records for ~1.4 million compounds tested against ~9,200 protein targets, curated from scientific literature and patent literature. BindingDB stores quantitative binding measurements (Ki, Kd, IC50, EC50) essential for drug discovery, pharmacology, and computational chemistry research.

**Key resources:**
- BindingDB website: https://www.bindingdb.org/
- REST API: https://www.bindingdb.org/axis2/services/BDBService
- Downloads: https://www.bindingdb.org/bind/chemsearch/marvin/Download.jsp
- GitHub: https://github.com/drugilsberg/bindingdb

## When to Use This Skill

Use BindingDB when:

- **Target-based drug discovery**: What known compounds bind to a target protein? What are their affinities?
- **SAR analysis**: How do structural modifications affect binding affinity for a series of analogs?
- **Lead compound profiling**: What targets does a compound bind (selectivity/polypharmacology)?
- **Benchmark datasets**: Obtain curated protein-ligand affinity data for ML model training
- **Repurposing analysis**: Does an approved drug bind to an unintended target?
- **Competitive analysis**: What is the best reported affinity for a target class?
- **Fragment screening**: Find validated binding data for fragments against a target

## Core Capabilities

### 1. BindingDB REST API

Base URL: `https://www.bindingdb.org/axis2/services/BDBService`

```python
import requests

BASE_URL = "https://www.bindingdb.org/axis2/services/BDBService"

def bindingdb_query(method, params):
    """Query the BindingDB REST API."""
    url = f"{BASE_URL}/{method}"
    response = requests.get(url, params=params, headers={"Accept": "application/json"})
    response.raise_for_status()
    return response.json()
```

### 2. Query by Target (UniProt ID)

The rest: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/blob/HEAD/skills/bindingdb-database/SKILL.md