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https://github.com/kull-centre/_2025_schulze_abundance-model

https://github.com/kull-centre/_2025_schulze_abundance-model

Science Score: 34.0%

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Basic Info
  • Host: GitHub
  • Owner: KULL-Centre
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 11 MB
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Created 11 months ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

2025Schulze_abundance-model

This repository contains data and scripts to reproduce results from the following preprint:

Thea K. Schulze, Lasse M. Blaabjerg, Matteo Cagiada, Kresten Lindorff-Larsen (2025) Supervised learning of protein variant effects across large-scale mutagenesis datasets. bioRxiv 2025.04.02.646878; doi: https://doi.org/10.1101/2025.04.02.646878

We provide example scripts and data to train and validate supervised models against VAMP-seq abundance scores:

  • /output/models.zip: A selection of pretrained models corresponding to those reported in the preprint.
  • /output/feature_set_1: Examples of scripts to run training and validation pipeline for different versions of our model architecture.
  • /data/df_vamp.csv: All training data (VAMP-seq scores for six different proteins) and model input features (structure-based features, including ESM-IF scores).

Owner

  • Name: Linderstrøm-Lang Centre for Protein Science, University of Copenhagen
  • Login: KULL-Centre
  • Kind: organization
  • Location: Copenhagen, Denmark

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