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tooluniverse-gpcr-structural-pharmacology

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GPCR receptor pharmacology — agonist/antagonist/inverse-agonist/biased-agonist classification, GPCRdb structural data, receptor-ligand binding analysis, antibody-target interface (SAbDab). Use for GPCR drug discovery, biased-agonism analysis, receptor subtype selectivity questions, and orthosteric vs allosteric pocket characterization.

skills/tooluniverse-gpcr-structural-pharmacology/SKILL.md

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# GPCR and Structural Pharmacology Research

**GPCR pharmacology**: agonist vs antagonist vs inverse agonist vs biased agonist — each has different clinical implications. Biased agonism (preferential G-protein vs β-arrestin signaling) can separate efficacy from side effects; for example, G-protein-biased opioid agonists aim to retain analgesia while reducing β-arrestin-mediated respiratory depression. Always classify retrieved ligands by their pharmacological type, not just their chemical structure. Receptor state (active vs inactive crystal structure) determines which ligands and mutations are interpretable — an inactive-state structure is appropriate for antagonist binding analysis, active-state for agonist-bound complexes. Generic GPCR numbering (Ballesteros-Weinstein) enables cross-receptor mutation comparison; always report positions in this system alongside sequence positions.

**LOOK UP DON'T GUESS**: never assume GPCRdb entry names (e.g., `adrb2_human`) or PDB IDs — always use `GPCRdb_list_proteins` to find the correct entry name and `GPCRdb_get_structures` to confirm available structures.

Research skill integrating GPCRdb (GPCR receptor biology), SAbDab (antibody structures), and PDBePISA (protein interface analysis) to support structural pharmacology, antibody engineering, and GPCR-targeted drug discovery.

**KEY PRINCIPLES**:
1. **Receptor-first** — Identify GPCR entry name before any GPCRdb queries
2. **Ligand classification** — Distinguish agonists, antagonists, partial agonists, biased agonists
3. **Structure-guided** — Pair GPCRdb mutation data with PDB structures via PDBePISA
4. **Antibody context** — Use SAbDab for therapeutic antibody structure retrieval and CDR analysis
5. **English-first queries** — Use standard receptor names (e.g., "beta-2 adrenergic receptor") in searches; convert to GPCRdb entry names for API calls
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