ersiliaos/eos69e6 repository overview

⁠Pharmacophore-guided molecular generation

Based on a molecules pharmacophore, this model generates new molecules de-novo to match the pharmacophore. Internally, pharmacophore hypotheses are generated for a given ligand. A graph neural network encodes spatially distributed chemical features and a transformer decoder generates molecules.

This model was incorporated on 2023-12-01.Last packaged on 2026-09-29.

⁠Information

⁠Identifiers

• Ersilia Identifier: eos69e6
• Slug: pgmg-pharmacophore

⁠Domain

• Task: Sampling
• Subtask: Generation
• Biomedical Area: Any
• Target Organism: Any
• Tags: Chemical graph model, Compound generation

⁠Input

• Input: Compound
• Input Dimension: 1

⁠Output

• Output Dimension: 100
• Output Consistency: Variable
• Interpretation: New molecules generated based on the pharmacophore

Below are the Output Columns of the model:

10 of 100 columns are shown

⁠Source and Deployment

• Source: Local
• Source Type: External
• DockerHub: https://hub.docker.com/r/ersiliaos/eos69e6⁠
• Docker Architecture: AMD64
• S3 Storage: https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos69e6.zip⁠

⁠Resource Consumption

• Model Size (Mb): 597
• Environment Size (Mb): 1611
• Image Size (Mb): 2212.9

Computational Performance (seconds):

• 10 inputs: 216.92
• 100 inputs: -1
• 10000 inputs: -1

⁠References

• Source Code: https://github.com/CSUBioGroup/PGMG⁠
• Publication: https://doi.org/10.1038/s41467-023-41454-9⁠
• Publication Type: Peer reviewed
• 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 CC-BY-NC-SA-4.0⁠ 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 eos69e6

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

# serve the model
ersilia serve eos69e6
# 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!