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alterlab-bindingdb

Query BindingDB drug-target affinities by UniProt IDs, compound names, or SMILES.

58|9|Updated Mar 16, 2026
Search Tags:#affinity#sar#drug-target#bindingdb#kd#ki#ic50
One-click install
npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-bindingdb
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alterlab-bindingdb
Source: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/databases/alterlab-bindingdb
Command: npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-bindingdb

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

BindingDB provides a centralized source of measured drug-target affinities (Ki, Kd, IC50, EC50). It enables researchers to quickly access target-ligand binding data for SAR, lead optimization, and cross-target selectivity analyses.

Core Features & Use Cases

  • Target-focused querying: retrieve ligands for a UniProt target to profile potency.
  • Compound-based searches: fetch affinities by compound name or SMILES for SAR exploration.
  • Data-driven workflows: compile multi-target datasets for ML models or SAR analysis across targets and organisms.

Quick Start

Use BindingDB to pull all Ki data for a specific target by UniProt ID or to fetch affinities for a compound of interest.

Frequently Asked Questions about alterlab-bindingdb

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

FAQPage Schema
How do I fetch drug-target binding affinity data from BindingDB for SAR analysis?▼

Retrieve drug-target binding affinities from BindingDB by querying UniProt target IDs or compound names and SMILES to extract Ki, Kd, IC50, and EC50 measurements for SAR analysis workflows.

Can I query BindingDB using a UniProt ID to profile target potency?▼

Yes, you can query BindingDB using a UniProt ID to retrieve associated ligands and their measured binding affinities, enabling target-centric potency profiling and cross-target selectivity analysis.

What's the best way to compile multi-target affinity datasets for ML models?▼

Compile multi-target affinity datasets for ML models by programmatically extracting binding data across UniProt targets and organisms, pulling Ki, Kd, IC50, and EC50 values from BindingDB.

Does BindingDB support compound-based searches using SMILES strings?▼

Yes, BindingDB supports compound-based searches using compound names or SMILES strings, allowing you to fetch measured affinities across targets for SAR exploration and lead optimization.

What binding affinity metrics are available when extracting drug-target interaction data?▼

Available binding affinity metrics include Ki, Kd, IC50, and EC50 values, extracted from BindingDB to support drug discovery research, pharmacology analysis, and cross-target selectivity studies.

When should I use BindingDB for cross-target selectivity analysis instead of other data sources?▼

Use BindingDB for cross-target selectivity analysis when you need centralized measured drug-target affinities across organisms and targets, supporting SAR workflows and lead optimization with standardized Ki, Kd, IC50, and EC50 data.

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