bindingdb-query
Query the BindingDB drug-target binding affinity database. Use whenever the user asks about protein-ligand binding data, affinity measurements (Ki, IC50, Kd, EC50), or wants to look up binding partners for a UniProt ID, PDB ID, or compound SMILES string.
npx skills add BioTender-max/awesome-bio-agent-skills --skill bindingdb --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 Query Skill Search BindingDB binding affinity records by any entity. Auto-detects type by pattern: | Input Pattern | Detected As | Example | API Endpoint | |---|---|---|---| | `P35355`, `Q9Y233` | UniProt ID | `P00533` (EGFR) | `getLigandsByUniprots` | | `1Q0L`, `3ANM` | PDB ID (4-char, digit-leading) | `1Q0L` | `getLigandsByPDBs` | | contains `=()#[]@/\` | SMILES string | `CC(=O)Oc1ccccc1C(O)=O` | `getTargetByCompound` | | fallback | treated as UniProt | — | `getLigandsByUniprots` | ## API | Function | Input | Returns | |---|---|---| | `search(entity, cutoff)` | single entity string | dict with `entity`, `type`, `hits`, `affinities` | | `search_batch(entities, cutoff)` | list of entity strings | dict[str, search_result] | | `summarize(result)` | search() output | compact multi-line text | | `to_json(result)` | search() output | list[dict] of affinity records | | `query_by_uniprot(ids, cutoff)` | UniProt ID(s), nM cutoff | list[dict] | | `query_by_pdb(ids, cutoff, identity)` | PDB ID(s), nM cutoff, % identity | list[dict] | | `query_by_smiles(smiles, cutoff)` | SMILES, similarity 0–1 | list[dict] | **Parameters** - `cutoff` (int): affinity threshold in nM (default 10 00
- API
- Usage
- Key Fields in Each Affinity Record
- Data Source
What does the bindingdb-query skill do?
Query the BindingDB drug-target binding affinity database. Use whenever the user asks about protein-ligand binding data, affinity measurements (Ki, IC50, Kd, EC50), or wants to look up binding partners for a UniProt ID, PDB ID, or compound SMILES string.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill bindingdb --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 BioTender-max/awesome-bio-agent-skills, a repository with 135 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.