bindingdb-database
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.
npx skills add LeonChaoX/qinyan-academic-skills --skill bindingdb-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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
- Overview
- When to Use This Skill
- Core Capabilities
- 1. BindingDB REST API
- 2. Query by Target (UniProt ID)
- 3. Query by Compound Name or SMILES
- 4. Download-Based Analysis (Recommended for Large Queries)
- 5. SAR Analysis
- 6. Polypharmacology Profile
- Query Workflows
- Workflow 1: Find Best Inhibitors for a Target
- Workflow 2: Selectivity Profiling
- Workflow 3: Machine Learning Dataset Preparation
- Key Data Fields
What does the bindingdb-database skill do?
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.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill bindingdb-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.