ersiliaos/eos4e40 repository overview

⁠Broad spectrum antibiotic activity

Predicts growth inhibition of Escherichia coli directly from chemical structure. Stokes and colleagues screened an FDA-approved drug library of 1,760 molecules plus 800 natural products, 2,335 compounds once deduplicated, at 50 micromolar and binarised the results at an 80% growth-inhibition cut-off to train a directed message-passing network augmented with RDKit descriptors. Ranking the Drug Repurposing Hub with it surfaced halicin, a preclinical antidiabetic that cleared infections in mice; a separate ZINC15 screen of over 107 million molecules gave eight further actives.

This model was incorporated on 2020-11-04.Last packaged on 2026-10-08.

⁠Information

⁠Identifiers

• Ersilia Identifier: eos4e40
• Slug: chemprop-antibiotic

⁠Domain

• Task: Annotation
• Subtask: Activity prediction
• Biomedical Area: Antimicrobial resistance
• Target Organism: Escherichia coli
• Tags: IC50, Antimicrobial activity, Chemical graph model

⁠Input

• Input: Compound
• Input Dimension: 1

⁠Output

• Output Dimension: 1
• Output Consistency: Fixed
• Interpretation: Probability of Escherichia coli growth inhibition, actives being compounds blocking 80% of growth at 50 micromolar.

Below are the Output Columns of the model:

⁠Source and Deployment

• Source: Local
• Source Type: External
• DockerHub: https://hub.docker.com/r/ersiliaos/eos4e40⁠
• Docker Architecture: AMD64, ARM64
• S3 Storage: https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos4e40.zip⁠

⁠Resource Consumption

• Model Size (Mb): 428
• Environment Size (Mb): 1489
• Image Size (Mb): 2793.93

Computational Performance (seconds):

• 10 inputs: 32.02
• 100 inputs: 44.59
• 10000 inputs: 1626.57

⁠References

• Source Code: http://chemprop.csail.mit.edu/checkpoints⁠
• Publication: https://doi.org/10.1016/j.cell.2020.01.021⁠
• Publication Type: Peer reviewed
• Publication Year: 2020
• Ersilia Contributor: miquelduranfrigola⁠

⁠License

This package is licensed under a GPL-3.0⁠ license. The model contained within this package is licensed under a MIT⁠ 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 eos4e40

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

# serve the model
ersilia serve eos4e40
# 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!