Fa Predictor

Welcome to the Fa predictor, a program for the prediction of Fa (fraction absorbed), Papp (permeability coefficient for Caco-2), and D-Sol (solubility near pH 7 by dried DMSO method).

SDF file

How to use

Upload molecule(s) as an SDF/MOL file and click the "Proceed" button.

• In preparing the input file, use Open Babel¹ (http://openbabel.org/wiki/Main_Page) to generate 2D coordinates.
• You can include up to 30 compounds in the input file. It takes about 20-30 seconds to complete the calculations for 10 compounds.
• The user uploaded lists and calculations are retained while the web browser session is active. All the data are deleted on exiting the browser.

The model information

Model	Type	Output	Dataset	Accuracy	Method	Descriptor
Fa class	3 class	Low (0-0.2) Moderate (0.2-0.7) High (0.7-1.0)	Esaki et al. 2	Accuracy: 0.836 Kappa: 0.560	RF3	CDK4 Mordred5 PaDEL6
Papp class	2 class	Low (< 10-5 cm/s) High (> 10-5 cm/s)	Esaki et al. 2	Accuracy: 0.810 Kappa: 0.601	R-SVM	CDK4 Mordred5 PaDEL6
D-Sol class	2 class	Low (< 10 μg/mL) High (> 10 μg/mL)	Esaki et al. 2	Accuracy: 0.811 Kappa: 0.628	L-SVM	CDK4 Mordred5 PaDEL6

For details please refer to Esaki et al. ²

References

1. O'Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R., Open Babel: An open chemical toolbox. J. Cheminform. 2011; 3:33.
2. Esaki, T., Ohashi, R., Watanabe, R., Natsume-Kitatani, Y., Kawashima, H., Nagao, C., Komura, H., Mizuguchi, K., Constructing an in silico three-class predictor of human intestinal absorption with Caco-2 permeability and dried-DMSO solubility. J. Pharm. Sci. 2019; 108(11):3630-3639.
3. Breiman, L., Random Forest. Machine Learn. 2001; 45(1):5-32.
4. Steinbeck, C.; Han, Y.; Kuhn, S.; Horlacher, O.; Luttmann, E.; Willighagen, E., The Chemistry Development Kit (CDK): an open-source Java library for chemo- and bioinformatics. J. Chem. Inf. Comput. Sci. 2003; 43(2):493-500.
5. Moriwaki, H.; Tian, Y. S.; Kawashita, N.; Takagi, T., Mordred: a molecular descriptor calculator. J. Cheminform. 2018; 10(1):4.
6. Yap, C. W., PaDEL-descriptor: an open source software to calculate molecular descriptors and fingerprints. J. Comput. Chem. 2011; 32(7):1466-1474.