ersiliaos/eos8vud repository overview

⁠SQUID 3D shape generation

Generates ten molecules matching the three-dimensional shape of a reference compound while allowing the chemistry to change, the essence of ligand-based scaffold hopping. SQUID, from Adams and Coley, uses an equivariant network so that generation respects rotation and translation, conditioning on shape rather than on the molecular graph. Because sampling is stochastic and shape is matched approximately, outputs vary between runs and still require assessment for synthetic feasibility.

This model was incorporated on 2024-05-01.Last packaged on 2026-09-23.

⁠Information

⁠Identifiers

• Ersilia Identifier: eos8vud
• Slug: squid

⁠Domain

• Task: Sampling
• Subtask: Generation
• Biomedical Area: Any
• Target Organism: Any
• Tags: Compound generation

⁠Input

• Input: Compound
• Input Dimension: 1

⁠Output

• Output Dimension: 10
• Output Consistency: Variable
• Interpretation: Ten generated molecules conditioned to match the three-dimensional shape of the input.

Below are the Output Columns of the model:

⁠Source and Deployment

• Source: Local
• Source Type: External
• DockerHub: https://hub.docker.com/r/ersiliaos/eos8vud⁠
• Docker Architecture: AMD64, ARM64
• S3 Storage: https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos8vud.zip⁠

⁠Resource Consumption

• Model Size (Mb): 371
• Environment Size (Mb): 2608
• Image Size (Mb): 3052.22

Computational Performance (seconds):

• 10 inputs: 32.24
• 100 inputs: 1487.02
• 10000 inputs: -1

⁠References

• Source Code: https://github.com/keiradams/SQUID⁠
• Publication: https://doi.org/10.48550/arXiv.2210.04893⁠
• Publication Type: Preprint
• Publication Year: 2023
• 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 eos8vud

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

# serve the model
ersilia serve eos8vud
# 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!