What is pKi?

The pKi of a molecule is a number that tells us how strongly a molecule can bind to a specific target in the body, like a protein or receptor. It’s short for the “negative logarithm of the inhibition constant (Ki). Think of a molecule as a key, and a protein in the body (like a receptor or enzyme) as a lock. The pKi tells us how good the key is at fitting into the lock and staying there. A higher pKi means the molecule binds more tightly to the target.

pKi=−log10​(Ki​)

Ki (inhibition constant) is a measure of how much of a substance (like a supplement or medicine) is needed to bind to a target (e.g., receptor or enzyme) and block or reduce its activity. Since Ki is usually a small number (often in nanomolar or micromolar range), we take the negative log to make it easier to compare. That gives us pKi, which puts things on a simple, readable scale.

In the body, medications need to bind to specific targets to have an effect—like blocking a pain receptor, or inhibiting an enzyme involved in cancer. If a compound has a high pKi, it means it can do its job at a lower concentration, which can mean better potency and potentially fewer side effects.

What is SMILES notation?

SMILES notation (Simplified Molecular Input Line Entry System) is a way to represent a chemical structure using a line of text made up of letters, numbers, and symbols. It tells you how atoms in a molecule are connected, and is commonly used in chemistry software and databases. Atoms are written using their chemical symbols (e.g., C for carbon, O for oxygen). Bonds are usually implied (single bonds) but double (=) and triple (#) bonds can be shown.

Ethanol (drinking alcohol): SMILES: CCO

SMILES is powerful because it lets computers store and analyze molecules using just text, without needing a drawing.

Where can I find the SMILES for a molecule?

Finding the SMILES notation for a molecule is simple as it’s the standard notation used in chemistry. For many of the better known supplements and pharmaceuticals, the SMILES can be found in its Wikipedia entry, under its Chemical and physical properties. However, for more obscure molecules, it may be necessary to defer to PubChem which is an extensive chemical database.

What receptor activity can the basic Zygos Model predict?

The free version of the Zygos model can generate predictions for many of the most commonly targeted receptor sites in supplements and pharmaceuticals, including serotonin and dopamine receptors.

While a Graph Neural Network (GNN) can make accurate predictions about a compound’s behaviour by learning patterns from molecular structures, it does have limitations. For example some biological targets (like well-studied receptors), there may be lots of data, leading to more reliable predictions. For less-researched sites, predictions can be less accurate due to limited or biased training examples.

Dopaminergic Activity	D(1A) dopamine receptor D(2) dopamine receptor D(3) dopamine receptor D(4) dopamine receptor (DAT) Sodium-dependent dopamine transporter
Serotonergic Activity (5-HT / 5-hydroxytryptamine)	5-HT receptor 1A 5-HT receptor 1B 5-HT receptor 1D 5-HT receptor 2A 5-HT receptor 2B 5-HT receptor 2C 5-HT receptor 4 5-HT receptor 6 5-HT receptor 7 (SERT) Sodium-dependent serotonin transporter
Adrenergic Activity	Alpha-1A adrenergic receptor     Alpha-1B adrenergic receptor Alpha-1D adrenergic receptor Alpha-2A adrenergic receptor Alpha-2C adrenergic receptor (NOR) Sodium-dependent noradrenaline transporter
Opioid Activity	Delta-type opioid receptor Kappa-type opioid receptor Mu-type opioid receptor
Cannabinoid	Cannabinoid receptor 1 Cannabinoid receptor 2

What receptor activity can the Advanced Zygos Model predict?

An exhaustive list of all the sites the Advanced Model binds to is considered proprietary information. In addition to the sites covered by the basic free model, some of the other sites included in the Advanced model are:

• Hormonal Targets: This includes targets such as the Androgen Receptor and Estrogen Receptor. Androgen receptors regulate genes involved in male traits, muscle growth, libido, and hair development. Estrogen receptors control genes involved in female reproductive function, bone density, and cell growth.
• Chemokine Receptors: Chemokine receptors are a type of protein found on the surface of certain cells—especially immune cells—that help the body detect and respond to chemical signals called chemokines. They are particularly relevant for immune responses, cancer and chronic diseases.
• Adenosine Receptors: Adenosine receptors are a group of cell surface proteins that respond to adenosine, a molecule involved in energy transfer (like ATP) and cellular signalling. When adenosine binds to these receptors, it helps regulate many important processes in the body, such as sleep and wakefulness.
• Acetylcholine Receptors: Acetylcholine receptors are proteins found on the surface of nerve and muscle cells that respond to acetylcholine, a key neurotransmitter involved in muscle activation, memory, and attention. Acetylcholine receptors are particularly relevant for treatments for Alzheimer’s disease.