ersiliaos/eos2xeq repository overview

⁠Antibiotic downselection criteria based on similarity to known antibiotics

Applies seven structural checks used to triage candidate antibiotics, flagging PAINS and Brenk alerts, Morgan-fingerprint Tanimoto similarity of 0.5 or more to a curated set of 559 known antibacterials, and nitrofuran, fluoroquinolone, carbapenem and beta-lactam motifs. Krishnan and colleagues applied them when searching for de novo antibiotics against Neisseria gonorrhoeae and Staphylococcus aureus, keeping compounds below the similarity cut-off. The activity, cytotoxicity and synthetic accessibility filters of that study are not reproduced here.

This model was incorporated on 2025-09-17.Last packaged on 2026-10-07.

⁠Information

⁠Identifiers

• Ersilia Identifier: eos2xeq
• Slug: antibiotics-downselection

⁠Domain

• Task: Annotation
• Subtask: Property calculation or prediction
• Biomedical Area: Antimicrobial resistance
• Target Organism: Staphylococcus aureus, Neisseria gonorrhoeae
• Tags: Antimicrobial activity

⁠Input

• Input: Compound
• Input Dimension: 1

⁠Output

• Output Dimension: 7
• Output Consistency: Fixed
• Interpretation: Seven binary flags, 1 meaning a match, covering structural alerts, antibiotic motifs and 0.5 Tanimoto similarity to 559 known antibacterials.

Below are the Output Columns of the model:

⁠Source and Deployment

• Source: Local
• Source Type: External
• DockerHub: https://hub.docker.com/r/ersiliaos/eos2xeq⁠
• Docker Architecture: AMD64, ARM64
• S3 Storage: https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos2xeq.zip⁠

⁠Resource Consumption

• Model Size (Mb): 1
• Environment Size (Mb): 539
• Image Size (Mb): 514.95

Computational Performance (seconds):

• 10 inputs: 28.6
• 100 inputs: 21.57
• 10000 inputs: 224.69

⁠References

• Source Code: https://github.com/aartikrish/de-novo-antibiotics/⁠
• Publication: https://doi.org/10.1016/j.cell.2025.07.033⁠
• Publication Type: Peer reviewed
• Publication Year: 2025
• Ersilia Contributor: miquelduranfrigola⁠

⁠License

This package is licensed under a GPL-3.0⁠ license. The model contained within this package is licensed under a Non-commercial⁠ 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 eos2xeq

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

# serve the model
ersilia serve eos2xeq
# 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!