ersiliaos/eos9x3z repository overview

⁠Gram-negative activity as a permeability proxy

Scores compounds for activity against Gram-negative bacteria, treated as a proxy for whether they penetrate the cell envelope. Gurvic and colleagues curated single-point MIC data from CDD and CO-ADD into 1,887 compounds, labelling those active against both Staphylococcus aureus and Escherichia coli as permeable and those active only against the Gram-positive organism as impermeable, then trained an ensemble of five Chemprop graph networks on that split. Since activity requires both entry and target engagement, a high value indicates the combination rather than permeability alone.

This model was incorporated on 2025-12-10.Last packaged on 2026-10-07.

⁠Information

⁠Identifiers

• Ersilia Identifier: eos9x3z
• Slug: gram-negative-permeability-proxy

⁠Domain

• Task: Annotation
• Subtask: Activity prediction
• Biomedical Area: Antimicrobial resistance
• Target Organism: Escherichia coli, Staphylococcus aureus
• Tags: Antimicrobial activity

⁠Input

• Input: Compound
• Input Dimension: 1

⁠Output

• Output Dimension: 1
• Output Consistency: Fixed
• Interpretation: Probability of Escherichia coli activity at a pMIC cut-off of 5, a Gram-negative permeability proxy.

Below are the Output Columns of the model:

⁠Source and Deployment

• Source: Local
• Source Type: External
• DockerHub: https://hub.docker.com/r/ersiliaos/eos9x3z⁠
• Docker Architecture: AMD64, ARM64
• S3 Storage: https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos9x3z.zip⁠

⁠Resource Consumption

• Model Size (Mb): 121
• Environment Size (Mb): 6187
• Image Size (Mb): 6493.9

Computational Performance (seconds):

• 10 inputs: 31.88
• 100 inputs: 31.57
• 10000 inputs: 765.27

⁠References

• Source Code: https://pubs.acs.org/doi/suppl/10.1021/acs.jmedchem.1c01984/suppl_file/jm1c01984_si_001.zip⁠
• Publication: https://doi.org/10.1021/acs.jmedchem.1c01984⁠
• Publication Type: Peer reviewed
• Publication Year: 2022
• Ersilia Contributor: miquelduranfrigola⁠

⁠License

This package is licensed under a GPL-3.0⁠ license. The model contained within this package is licensed under a GPL-3.0-or-later⁠ 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 eos9x3z

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

# serve the model
ersilia serve eos9x3z
# 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!