Small molecule properties

We compute or load a number of small molecule properties. These are related to metadata fields, but ones we describe here are generally higher-level computations. To view them, click (todo). Data will display in the lower portion of the sidebar.

LogP

Molar Refractivity (MR)

Polarizable surface area (TPSA)

We compute this in two ways. A: traditional heuristic approach, similar to that computed by RDKit. This is useful when comparing values to that used in other tools, including for ML applications.

B: Geometrically. This is more accurate for practical applications, as it takes into account 3d molecule geometry. We compute a mesh using the molecule's Van der Waals radii, then, sum area over any of its faces near Oxygen or Nitrogen atoms, or Hydrogen atoms covalently bonded to one. In practice, these results come out similar.

[Solvent] Acessible surface area (SAS)

We compute and display this in two ways. A: Using the traditional Labute heuristic. This is similar to how RdKit computes it. B: Geometrically. This is similar to TPSA above, but sums over every triangle in the mesh; not just ones near a polar molecule. In practice, these results come out similar.

Solubilty in water

We compute this using machine learning from the AqMolDb dataset. See the solubility page for details.