References

Everything this site is built on, in one place: the paper the method comes from, the work that revisits it, the data sources and the toolkit. If a number on this site is not traceable to something on this page, it should not be on this site.

The original method

Wessel MD, Jurs PC, Tolan JW, Muskal SM. Prediction of human intestinal absorption of drug compounds from molecular structure. Journal of Chemical Information and Computer Sciences 1998;38(4):726-735. doi:10.1021/ci980029a

86 compounds, 728 descriptors reduced to 127, a genetic algorithm choosing six for a 6-4-1 neural network, and reported errors of 9.4 training and 16.0 on a held-out set of ten. This is the model reproduced on How it works.

The current work

Muskal SM. Human Intestinal Absorption Revisited: A Genetic Algorithm Twenty Eight Years On. In preparation.

The reproduction of the 1998 model, the search over 1,301 modern descriptors and 781 compounds, the ceiling set by disagreement among published labels, the applicability flag, and the two cyclic peptide arms. Every measured number quoted on this site comes from this work. When it is posted, its identifier will be added here and to llms.txt.

Data sources

CycPeptMPDB, the Cyclic Peptide Membrane Permeability Database. cycpeptmpdb.com

The source of both peptide arms: 1,281 peptides measured on Caco-2 monolayers and 7,298 measured on artificial membranes of the PAMPA class. The two are different assays on different populations and are kept apart throughout, here and in the service.

The absorption labels are published human percent-absorbed measurements collected from the primary literature, 783 compounds of which 781 carry a continuous label. Where a compound carries several published values, the median is used and the spread is reported rather than discarded. The per-compound provenance travels with the table and will be published with it on Download.

Toolkit

RDKit: open source cheminformatics. rdkit.org

Every descriptor on this site is computed with RDKit, including the reimplementations of the six 1998 descriptors, which were rebuilt from their written definitions because the software that computed them in 1998 no longer runs. The exact pinned version travels with each prediction and is reported by the service.

Ketcher, the structure editor embedded on Try it and Peptides, vendored and served from this site rather than loaded from a third party.

How to cite

For the original method, cite the 1998 paper. For anything computed on this site, cite the paper in preparation and say which model and which arm you used, because the two peptide arms are separate models and a result from one is not a result from the other.

If you quote a prediction, quote its interval and its applicability band with it. A value from this site without its interval is not a result this site produced.