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bindingdb-database

Retrieve BindingDB drug-target binding affinities by UniProt or ligand identifiers.

94|11|Updated Mar 26, 2026
Search Tags:#bioinformatics#data-analysis#drug-discovery#sar#bindingdb#binding-affinity
One-click install
npx skills add https://github.com/swaruplab/operon --skill bindingdb-database-swaruplab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bindingdb-database
Source: https://github.com/swaruplab/operon/tree/main/src-tauri/protocols/bindingdb-database
Command: npx skills add https://github.com/swaruplab/operon --skill bindingdb-database-swaruplab

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Retrieve BindingDB binding affinity data (Ki, Kd, IC50, EC50) by target UniProt ID or ligand identifiers to support drug discovery, SAR analysis, and benchmarking.

Core Features & Use Cases

  • Target-centric data retrieval: fetch Ki, Kd, IC50, and EC50 values by UniProt ID or ligand.
  • SAR & lead profiling: compare affinities across targets and compounds to identify potent binders.
  • Dataset preparation: assemble clean, human-targeted affinity datasets for ML or benchmarking.

Quick Start

Query BindingDB for Ki data on UniProt ID P00519 and summarize the results.

Frequently Asked Questions about bindingdb-database

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

FAQPage Schema
How do I retrieve drug-target binding affinity data from BindingDB using a UniProt ID?▼

You can retrieve drug-target binding affinity data by querying the BindingDB REST API with a specific UniProt ID. The Skill parses the API responses to extract Ki, Kd, IC50, and EC50 measurements for the requested target.

Can I normalize BindingDB affinity values to a nanomolar scale for cross-target comparisons?▼

Yes, normalizing BindingDB affinity values to a nanomolar scale is supported. The Skill handles unit normalization during response parsing to ensure consistent comparisons across different targets and compounds in SAR analysis.

What is the best way to prepare a clean binding affinity dataset for machine learning from BindingDB?▼

To prepare an ML dataset from BindingDB, query the REST API by target UniProt ID or ligand identifier. The Skill fetches and parses the affinity data, providing a clean dataset ready for benchmarking and machine learning applications.

Does this approach support target-centric SAR analysis and lead profiling?▼

Target-centric SAR analysis and lead profiling are fully supported. By retrieving and comparing binding affinities across multiple targets and compounds, you can identify potent binders and profile leads effectively.

Do I need a BindingDB API key to fetch IC50 and EC50 measurements?▼

The Skill requires access to the BindingDB REST API to fetch IC50 and EC50 measurements. It processes the API responses to extract and normalize the affinity values for your drug discovery and benchmarking tasks.

Can I fetch binding affinity data by ligand identifier instead of UniProt target ID?▼

Yes, you can fetch binding affinity data by ligand identifier. The Skill supports querying BindingDB using either a UniProt target ID or a ligand identifier to retrieve relevant Ki, Kd, IC50, and EC50 values.

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