ersiliaos/eos1af5 repository overview

⁠Coloring molecules for Caco-2 cell permeability

Estimates apparent permeability across a Caco-2 monolayer, the in vitro gold-standard proxy for how readily an orally dosed compound crosses the intestinal wall. Values come back as the negative log10 of Papp in cm/s, so a higher number means a less permeable compound. Jimenez-Luna and colleagues fitted a message-passing graph neural network, paired with integrated-gradients colouring of the atoms behind each prediction, to 239 compounds pooled from two studies. With so little data and a cross-validated Pearson R of 0.53, treat the output as a ranking aid.

This model was incorporated on 2021-10-19. Last packaged on 2026-11-03.

⁠Information

⁠Identifiers

• Ersilia Identifier: eos1af5
• Slug: molgrad-caco2

⁠Domain

• Task: Annotation
• Subtask: Activity prediction
• Biomedical Area: ADMET
• Target Organism: Homo sapiens
• Tags: Permeability, ADME, Papp, Chemical graph model

⁠Input

• Input: Compound
• Input Dimension: 1

⁠Output

• Output Dimension: 1
• Output Consistency: Fixed
• Interpretation: Negative log10 of Caco-2 apparent permeability in cm/s, where lower values indicate greater permeability.

Below are the Output Columns of the model:

⁠Source and Deployment

• Source: Local
• Source Type: External
• DockerHub: https://chstno1.isgood.host/r/ersiliaos/eos1af5⁠
• Docker Architecture: AMD64
• S3 Storage: https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos1af5.zip⁠

⁠Resource Consumption

• Model Size (Mb): 17
• Environment Size (Mb): 2414
• Image Size (Mb): 2330.42

Computational Performance (seconds):

• 10 inputs: 24.46
• 100 inputs: 16.14
• 10000 inputs: 162.74

⁠References

• Source Code: https://github.com/josejimenezluna/molgrad/⁠
• Publication: https://doi.org/10.1021/acs.jcim.0c01344⁠
• Publication Type: Peer reviewed
• Publication Year: 2021
• Ersilia Contributor: miquelduranfrigola⁠

⁠License

This package is licensed under a GPL-3.0⁠ license. The model contained within this package is licensed under a AGPL-3.0-only⁠ license.

Notice: Ersilia grants access to models as is, directly from the original authors, please refer to the original code repository and/or publication if you use the model in your research.

⁠Use

To use this model locally, you need to have the Ersilia CLI⁠ installed. The model can be fetched using the following command:

# fetch model from the Ersilia Model Hub
ersilia fetch eos1af5

Then, you can serve, run and close the model as follows:

# serve the model
ersilia serve eos1af5
# generate an example file
ersilia example -n 3 -f my_input.csv
# run the model
ersilia run -i my_input.csv -o my_output.csv
# close the model
ersilia close

⁠About Ersilia

The Ersilia Open Source Initiative⁠ is a tech non-profit organization fueling sustainable research in the Global South. Please cite⁠ the Ersilia Model Hub if you've found this model to be useful. Always let us know⁠ if you experience any issues while trying to run it. If you want to contribute to our mission, consider donating⁠ to Ersilia!