ersiliaos/eos3lyd repository overview

⁠Efflux pump avoidance in gram-negative bacteria

Estimates whether a compound slips past the multidrug efflux pumps that expel antibacterials from Gram-negative cells, one of the two barriers, alongside outer membrane permeability, that keeps most chemistry from reaching its target. Gurvic and Zachariae compared growth inhibition of 73,737 CO-ADD compounds across wild-type, efflux-deficient tolC and hyperpermeable lpxC Escherichia coli, labelling 186 as efflux evaders and 554 as substrates. Ersilia trained the classifier served here on those two classes. Evading efflux does not by itself confer antibacterial activity.

This model was incorporated on 2025-12-12.Last packaged on 2026-10-26.

⁠Information

⁠Identifiers

• Ersilia Identifier: eos3lyd
• Slug: efflux-avoidance-gram-negative

⁠Domain

• Task: Annotation
• Subtask: Activity prediction
• Biomedical Area: Antimicrobial resistance, Diarrheal diseases
• Target Organism: Escherichia coli
• Tags: Antimicrobial activity, Gram-negative bacteria

⁠Input

• Input: Compound
• Input Dimension: 1

⁠Output

• Output Dimension: 1
• Output Consistency: Fixed
• Interpretation: Rank score of evasion of TolC-dependent efflux in Escherichia coli calibrated against the Ersilia reference library of 50K compounds. A score above 0.65 beats 99% of that library. Trained on 186 evaders against 554 substrates.

Below are the Output Columns of the model:

⁠Source and Deployment

• Source: Local
• Source Type: Internal
• DockerHub: https://hub.docker.com/r/ersiliaos/eos3lyd⁠
• Docker Architecture: AMD64, ARM64
• S3 Storage: https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos3lyd.zip⁠

⁠Resource Consumption

• Model Size (Mb): 11
• Environment Size (Mb): 7512
• Image Size (Mb): 7541.73

Computational Performance (seconds):

• 10 inputs: 40.06
• 100 inputs: 30.82
• 10000 inputs: 667.84

⁠References

• Source Code: https://github.com/domgurvic/efflux_evaders_and_substrates⁠
• Publication: https://doi.org/10.1038/s44259-024-00023-w⁠
• Publication Type: Peer reviewed
• Publication Year: 2024
• Ersilia Contributor: miquelduranfrigola⁠

⁠License

This package is licensed under a GPL-3.0⁠ license. The model contained within this package is licensed under a Apache-2.0⁠ 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 eos3lyd

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

# serve the model
ersilia serve eos3lyd
# 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!