Every entry has: approval badge (legal status) · evidence stars (human-evidence strength) · technical mechanism (the gene/receptor pathway) · molecular target (official links: [NCBI Gene] for the gene, [PubChem] for the molecule, [Mol\*/PDB] for the 3D structure) · plain English · protocol/watch-out/bottom-line.
Core glossary (every term used across the wiki — bookmark this):
- Agonist / Antagonist — activates / blocks a receptor
- Ligand — any molecule that binds a receptor
- Receptor — protein that receives a signal (GPCR, nuclear, ion-channel)
- Enzyme — protein that speeds a reaction (drugs often inhibit them)
- Transporter — membrane door that moves molecules in/out
- Kinase / Phosphorylation — enzyme that adds a phosphate = the cell's on/off switch
- Transcription / Translation — DNA→mRNA / mRNA→protein
- Upregulate / Downregulate — make more / less of a protein
- Gene expression — how much a gene is being used
- Half-life — time for blood level to halve
- Bioavailability — fraction reaching the bloodstream
- First-pass — liver destroying an oral dose before circulation
- CYP450 — liver enzymes that metabolize drugs (interaction source)
- Second messenger (cAMP) — the internal relay after a receptor fires
- Selectivity — how few off-targets a drug hits
- Tolerance / Downregulation — receptors removed after overstimulation
- Therapeutic index — safety gap between effective and toxic dose
- RCT / meta-analysis — the gold-standard evidence forms
- Effect size / p-value — how big / how likely-real a result is
- In vitro / in vivo — in a dish / in a living body
- HPTA — hypothalamic-pituitary-testicular axis (the testosterone control loop steroids suppress)
- HPA axis — hypothalamic-pituitary-adrenal axis (the cortisol/stress loop)
The visualization toolkit (free, embeddable — used across the site)
- Compound structure (2D + 3D): PubChem — every molecule, embeddable.
- Protein/receptor 3D structure: Mol\* at RCSB PDB — open-source viewer (built by the Protein Data Bank, used by AlphaFold), embeds in-browser. See the actual fold of the androgen receptor, VEGFR2, mTOR.
- Protein sequence & domains: UniProt — the amino-acid chain and functional regions of any protein.
- Predicted structures: AlphaFold DB — 3D predictions for proteins without experimental structures.
- Pathway maps: Reactome and KEGG — the wiring diagrams for the Pathways module.
Next: the Pathways module — the ~15 master cascades every compound plugs into.
✅ Key takeaways
- Every compound page carries: approval badge (legal status) · evidence stars (HUMAN-evidence strength) · technical mechanism (gene/receptor) · molecular target (official links) · plain English · protocol / watch-out / bottom-line.
- The glossary is your key: agonist/antagonist, ligand, kinase/phosphorylation, transcription/translation, half-life, bioavailability, CYP450, therapeutic index, RCT/meta-analysis.
- The visualization toolkit (PubChem, Mol*/RCSB PDB, UniProt, AlphaFold, Reactome/KEGG) lets you see the actual molecule, protein fold, and pathway — all free.
🧠 Check yourself
Q1 On a compound page, what do the evidence stars measure — and what tag must an animal-only compound carry?
The strength of HUMAN evidence. Animal-only data is capped at ⭐⭐ and must say 'animal'.
Q2 Where would you go to see the real 3D fold of a receptor like the androgen receptor?
Mol* at RCSB PDB (the Protein Data Bank's in-browser viewer). PubChem shows small-molecule structures; AlphaFold predicts proteins that lack an experimental structure.