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1. ParisaH-Lab/CyclicMPNN ParisaH-Lab/CyclicMPNN Public

   A fine-tuned version of ProteinMPNN for generating stable cyclic peptide sequences

   Jupyter Notebook 52 15

2. UsefulRosettaScripts UsefulRosettaScripts Public

   Here are some Rosetta based scripts that I have made that are general enough they may be useful for something within your project! Enjoy :)

   Python 6

3. openmm-scripts openmm-scripts Public

   Helpful python scripts written to be able to easily submit an MD trajectory submitted to either a GPU or CPU on a cluster or local pc.

   Python 3 1

4. MLModules MLModules Public

   Here are modular ML portions that I have written for myself, but included jupyter notebook examples explaining them. Hopefully you find them useful!

   Jupyter Notebook

5. Zach-Sisson-1/Host-Pathogen_Network_Analysis Zach-Sisson-1/Host-Pathogen_Network_Analysis Public

   Project in collaboration with Parisa Hosseinzadeh at the University of Oregon investigating the sub-network of interactions between pathogen and human proteins

   Jupyter Notebook 2

6. Demultiplex Demultiplex Public

   Tool to Demultiplex and determine the level of index swapping and undetermined index-pairs, before and after quality filtering of index reads.

   Python 1 1