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1. RosettaCommons/atomworks RosettaCommons/atomworks Public

   A generalized computational framework for biomolecular modeling.

   Python 428 46

2. RosettaCommons/foundry RosettaCommons/foundry Public

   Central repository for biomolecular foundation models with shared trainers and pipeline components

   Python 865 161

3. chaitjo/geometric-gnn-dojo chaitjo/geometric-gnn-dojo Public

   Geometric GNN Dojo provides unified implementations and experiments to explore the design space of Geometric Graph Neural Networks (ICML 2023)

   Jupyter Notebook 525 55

4. pymol-remote pymol-remote Public

   Send data to and from pymol from a remote server (e.g. a cluster running deep learning workflows)

   Python 38 2

5. a-r-j/ProteinWorkshop a-r-j/ProteinWorkshop Public

   Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

   Python 274 22

6. Hollfelder-Lab/lrDMS-IRED Hollfelder-Lab/lrDMS-IRED Public

   Code, data and notebooks for engineering enzymes with ultra-high throughput microfluidics. Please read our accompanying paper for details.

   Jupyter Notebook 11 2