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bindingdb-database

Retrieves binding affinity data from BindingDB by target or compound.

48|6|Updated Mar 9, 2026
Search Tags:#pubchem#drug-discovery#chembl#SAR#uniprot#bindingdb#binding-affinity
One-click install
npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill bindingdb-database-qinyan-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bindingdb-database
Source: https://github.com/qinyan-ai/qinyan-academic-skills/tree/main/skills/12-%E7%A7%91%E5%AD%A6%E6%95%B0%E6%8D%AE%E5%BA%93/bindingdb-database
Command: npx skills add https://github.com/qinyan-ai/qinyan-academic-skills --skill bindingdb-database-qinyan-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill enables researchers to retrieve measured drug-protein binding affinities for targets and compounds from BindingDB, eliminating manual lookups and data collection.

Core Features & Use Cases

  • Target-based queries: fetch ligands and affinities for a UniProt target.
  • Compound-centric searches: look up affinities by compound name or SMILES.
  • Data fields & export: obtain Ki, Kd, IC50, EC50 values along with Ligand SMILES, PubChem CID, and ChEMBL IDs for downstream analysis.
  • Use case: perform SAR profiling for a kinase by gathering affinities across multiple ligands.

Quick Start

Query BindingDB for a target or compound and export the results to CSV.

Frequently Asked Questions about bindingdb-database

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

FAQPage Schema
How do I retrieve binding affinity data from BindingDB for a specific drug target?▼

To retrieve binding affinity data from BindingDB, query a specific drug target using its UniProt ID. The Skill returns measured affinities including Ki, Kd, IC50, and EC50 values, alongside ligand SMILES and identifiers.

Can I look up compound binding affinities using a SMILES string?▼

You can perform compound-centric searches by inputting a SMILES string or compound name. This retrieves binding affinities and associated identifiers like PubChem CID and ChEMBL IDs for downstream analysis.

What is the best way to gather ligand affinities for SAR profiling?▼

Gathering ligand affinities for SAR profiling requires querying BindingDB for a target protein across multiple ligands. This Skill fetches Ki, Kd, IC50, and EC50 values to support structure-activity relationship analysis.

Does this BindingDB query tool return PubChem and ChEMBL IDs?▼

Yes, querying BindingDB through this tool returns structured results that include PubChem CID and ChEMBL IDs. It also provides Ligand SMILES and affinity measurements for comprehensive data export.

How do I export binding affinity results to CSV for downstream analysis?▼

After querying BindingDB for targets or compounds, you can export the structured results to CSV. This format captures Ki, Kd, IC50, EC50 values, and chemical identifiers for analysis.

What binding affinity metrics can I fetch for drug discovery targets?▼

For drug discovery targets, you can fetch standard binding affinity metrics including Ki, Kd, IC50, and EC50 values. These are retrieved from BindingDB using target or compound queries.

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