Research

The measured biology of the plants we carry

Tradition tells us which plants matter. To say why, we follow each one down to the molecules it carries, the proteins those molecules meet, and the measurements that record the meeting. These are our investigations — every molecular claim traced to a primary source, structure and function only.

Behind every plant sits a genome engine — 16,000+ cited molecular relationships across the graph, including 3,388 directly measured binding affinities. Each edge carries its evidence tier — measured, literature-recorded, occurrence, or computed — and the strongest are the ones we measured.

3,388
Measured binding affinities
from BindingDB — compounds measured against their protein targets
3,908
Plant → compound edges
Dr. Duke's phytochemical record, by botanical binomial
6,142
Compound occurrences
LOTUS — which plant carries which molecule, in nature
234
Protein structures
AlphaFold — the folded shape of each target the molecules meet

Chemistry

PubChem · ChEMBL · Dr. Duke's Phytochemical DB · COCONUT · LOTUS

Measured binding

BindingDB · PubChem BioAssay

Protein structure

AlphaFold2 · OpenFold2 · RCSB PDB

Expression → body

Human Protein Atlas · GTEx · UniProt

Literature

Europe PMC (cited + verified)

Tradition

Culpeper (1653) · Classical TCM · Old English Herbals

The source databases are the field’s own — but assembling measured binding, structure, expression, and the recorded herbal tradition into one cited, live-computed graph, and publishing it for a whole apothecary catalog, is something no consumer botanical brand we know of ships. That graph is the institute. Structure and function only; not a claim to treat, cure, or prevent any disease.

The convergence standard · our defining evidence

Where the molecule and the tradition independently agree

This is the hardest thing in the institute to replicate, and the thing we are proudest of. It takes two independent evidence systems — a measured molecular graph and a structured corpus of recorded herbal tradition — and finds where they meet on their own. When a plant’s compounds are measured to engage the genes of an organ, and the recorded lineage already named that plant for that same organ, the two agree without being made to. We know of no other botanical brand that holds both halves, so no other can show this. 93such convergences stand in the genome today — every one backed by an actual measured binding affinity, not annotation alone. Two sources, arrived at separately, is our highest standard of evidence.

Immune

Agaricus Blazei · andrographis · Astragalus · Burdock · Chaga · chinese-skullcap · Clove · Eleuthero · feverfew · garlic · goldenseal · Morinda · oregano · Reishi · Siberian Ginseng · thyme · Tulsi (Holy Basil) · turmeric

Nervous

Albizia · Asparagus Root · Eleuthero · Hemp Leaf · Jujube · Longan Berry · magnolia · peppermint · Polygala · Reishi · rosemary · Siberian Ginseng · Tulsi (Holy Basil)

Metabolic

American Ginseng · Astragalus · Cinnamon · Codonopsis · Eleuthero · green-tea · Gynostemma · Moringa · Mulberry · Rhodiola · Siberian Ginseng · soy

Respiratory

Asparagus Root · chinese-skullcap · Codonopsis · garlic · Ginger · Licorice · magnolia · Mulberry · oregano · peppermint · thyme · Tulsi (Holy Basil)

Liver & Detox

andrographis · Burdock · chinese-skullcap · Dandelion · Goji Berry · He Shou Wu (Fo-Ti) · rosemary · Schizandra · turmeric · Wheat Grass

Digestive

bayberry · celery · hawthorn · oregano · peppermint · pomegranate · rosemary · strawberry

Cardiovascular

bayberry · garlic · green-tea · hawthorn · Longan Berry · pomegranate · soy

Endocrine

Eleuthero · He Shou Wu (Fo-Ti) · Licorice · Morinda · Moringa · soy

Antioxidant & Longevity

broccoli-sprout · green-tea · He Shou Wu (Fo-Ti) · pomegranate · Wheat Grass

Skin & Connective

Burdock · Morinda

marks a convergence backed by a measured binding affinity (BindingDB), not annotation alone. Convergence describes where independent lines of evidence meet on a body system. It is structure and function only, not a claim to treat, cure, or prevent any disease.

The atlas · The method

The Clarity Atlas

A measured target-engagement map of every botanical we read — each herb’s molecules traced to the human proteins they are measured, in ChEMBL, to interact with. Honest numbers, plain-language method, and a clear account of where the map stops. Measured, not clinical; structure and function only.

Read the atlas ↗

Methods · Start here

How we read a plant

Tradition tells us which plants matter. To say why, we follow each one down to the molecules it carries, the proteins those molecules meet, and the measurements that record the meeting — in the open, every step cited.

Read the method ↗

The series

Measured Biology

One investigation per plant — the active compounds, the proteins each is measured to engage, and, where we have computed it, the predicted binding geometry from our own molecular docking.

Measured Biology

The Measured Biology of Agaricus Blazei

Agaricus Blazei (Agaricus blazei Murill) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Asparagus Root

Asparagus Root (Asparagus cochinchinensis) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Astragalus

Astragalus (Astragalus membranaceus) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Burdock

Burdock (Arctium lappa) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Cistanche

Cistanche (Cistanche deserticola) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Cordyceps

Cordyceps (Cordyceps militaris) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Eleuthero

Eleuthero (Eleutherococcus senticosus) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Ginger

Ginger (Zingiber officinale) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Goji Berry

Goji Berry (Lycium barbarum) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Jamaican Purple Sea Moss

Jamaican Purple Sea Moss (Eucheuma cottonii / Gracilaria spp.) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Mulberry

Mulberry (Morus alba) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Polygala

Polygala (Polygala tenuifolia) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Red Asparagus

Red Asparagus (Asparagus officinalis (red variety)) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Reishi

Reishi (Ganoderma lucidum) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Siberian Ginseng

Siberian Ginseng (Eleutherococcus senticosus) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Turkey Tail

Turkey Tail (Trametes versicolor) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Wheat Grass

Wheat Grass (Triticum aestivum) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Albizia

Albizia (Albizia julibrissin) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of American Ginseng

American Ginseng (Panax quinquefolius) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Atlantic Irish Sea Moss

Atlantic Irish Sea Moss (Chondrus crispus) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Bladderwrack

Bladderwrack (Fucus vesiculosus) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Chaga

Chaga (Inonotus obliquus) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Cinnamon

Cinnamon (Cinnamomum cassia) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Clove

Clove (Syzygium aromaticum) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Codonopsis

Codonopsis (Codonopsis pilosula) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Dandelion

Dandelion (Taraxacum officinale) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Dendrobium

Dendrobium (Dendrobium nobile) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Eucommia

Eucommia (Eucommia ulmoides) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Gynostemma

Gynostemma (Gynostemma pentaphyllum) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of He Shou Wu (Fo-Ti)

He Shou Wu (Fo-Ti) (Polygonum multiflorum) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Jatamansi (Spikenard)

Jatamansi (Spikenard) (Nardostachys jatamansi) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Jujube

Jujube (Ziziphus jujuba) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Licorice

Licorice (Glycyrrhiza glabra) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Lion's Mane

Lion's Mane (Hericium erinaceus) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Longan Berry

Longan Berry (Dimocarpus longan) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Morinda

Morinda (Morinda citrifolia) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Moringa

Moringa (Moringa oleifera) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Purple Mulberry

Purple Mulberry (Morus nigra) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Rehmannia

Rehmannia (Rehmannia glutinosa) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Rhodiola

Rhodiola (Rhodiola rosea) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Schizandra

Schizandra (Schisandra chinensis) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Spirit Poria

Spirit Poria (Wolfiporia extensa) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.

Measured Biology

The Measured Biology of Tulsi (Holy Basil)

Tulsi (Holy Basil) (Ocimum sanctum) — the compounds it carries, the proteins they are measured to engage, and the points where the plant meets your biology.