ersiliaos/eos4q1a repository overview

⁠CReM fragment based structure generation

CReM (chemically reasonable mutations) is a fragment-based generative model that breaks a molecule into fragments and replaces them with fragments from a database. It supports three modes: MUTATE (replace a fragment), GROW (replace a hydrogen with a fragment), and LINK (link two molecules via a fragment). This model uses MUTATE and GROW, which can generate thousands of analogues. When more than 100 molecules are generated, 100 diverse representatives are selected using Mini Batch K-Means clustering.

This model was incorporated on 2022-12-15.Last packaged on 2026-09-23.

⁠Information

⁠Identifiers

• Ersilia Identifier: eos4q1a
• Slug: crem-structure-generation

⁠Domain

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

⁠Input

• Input: Compound
• Input Dimension: 1

⁠Output

• Output Dimension: 100
• Output Consistency: Variable
• Interpretation: Up to 100 newly generated molecules

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/eos4q1a⁠
• Docker Architecture: AMD64, ARM64
• S3 Storage: https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/eos4q1a.zip⁠

⁠Resource Consumption

• Model Size (Mb): 688
• Environment Size (Mb): 661
• Image Size (Mb): 2693.47

Computational Performance (seconds):

• 10 inputs: 31.19
• 100 inputs: 476.76
• 10000 inputs: -1

⁠References

• Source Code: https://github.com/DrrDom/crem⁠
• Publication: https://doi.org/10.1186/s13321-020-00431-w⁠
• Publication Type: Peer reviewed
• Publication Year: 2020
• Ersilia Contributor: DhanshreeA⁠

⁠License

This package is licensed under a GPL-3.0⁠ license. The model contained within this package is licensed under a BSD-3-Clause⁠ 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 eos4q1a

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

# serve the model
ersilia serve eos4q1a
# 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!