SARS-CoV inhibition

This model was developed to support the early efforts in the identification of novel drugs against SARS-CoV2. It predicts the probability that a small molecule inhibits SARS-3CLpro-mediated peptide cleavage. It was developed using a high-throughput screening against the 3CL protease of SARS-CoV1, as no data was yet available for the new virus (SARS-CoV2) causing the COVID-19 pandemic. It uses the ChemProp model.

This model was incorporated on 2021-06-03.

Information

Identifiers

• Ersilia Identifier: eos9f6t
• Slug: chemprop-sars-cov-inhibition

Domain

• Task: Annotation
• Subtask: Activity prediction
• Biomedical Area: COVID-19
• Target Organism: SARS-CoV-2
• Tags: COVID19, Antiviral activity, Sars-CoV-2, Chemical graph model

Input

• Input: Compound
• Input Dimension: 1

Output

• Output Dimension: 1
• Output Consistency: Fixed
• Interpretation: Probability of 3CL protease inhibition (%) The classifier was trained using a threshold of 12% of inhibition

Below are the Output Columns of the model:

Name	Type	Direction	Description
activity	float	high	Probability of inhibiting SARS-CoV-1

Source and Deployment

• Source: Local
• Source Type: External
• DockerHub: https://hub.docker.com/r/ersiliaos/eos9f6t
• Docker Architecture: AMD64
• S3 Storage: https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos9f6t.zip

Resource Consumption

• Model Size (Mb): 9
• Environment Size (Mb): 5839
• Image Size (Mb): 5743.71

Computational Performance (seconds):

• 10 inputs: 55.57
• 100 inputs: 54.21
• 10000 inputs: -1

References

• Source Code: http://chemprop.csail.mit.edu/checkpoints
• Publication: https://pubmed.ncbi.nlm.nih.gov/32084340/
• 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 eos9f6t

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

# serve the model
ersilia serve eos9f6t
# 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!