This repository maintains important files/scripts for running or analyzing MD simulations of different insulin wild-type models and their glycovariants.
The paper of the project is published in the Journal of Computer-Aided Molecular Design (JCAMD), titled as Identifying signatures of proteolytic stability and monomeric propensity in O-glycosylated insulin using molecular simulation.
There are the following directories in this repository. Note that we don't store simulation outputs due to the huge file sizes. For more details about the files in each folder, please refer to the README file in each folder.
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JCAMD_paper: LaTex-relevant files for different versions of the paper submitted to the Journal of Computer-Aided Molecule Design (JCAMD). -
data_analysis: A folder containing analysis scripts and results for the figures in the main text and the SI and some additional analyses. -
glyco_insulin/: A folder containing the GLYCAM outputs of all the glyco-variants and a Python script for comparing glyco-variants built on different wild-type models. -
references: The work plan, project description and two directly relevant papers. -
useful_files: Useful files for preparing MD simulations for insulin wild-type and it glyco-variants. -
wildtype_insulin/: A folder containing the outputs of parameterizing each wild-type model using the H++ server.
- Wei-Tse Hsu ([email protected])
- Dominique A. Ramirez ([email protected])