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Public Github Repository for the following July 23, 2021 publication

Title: Formulation and Efficacy of Catalase-Loaded Nanoparticles for the Treatment of Neonatal Hypoxic-Ischemic Encephalopathy

Link to publication found here

This repository contains the necessary MD simulation files and in-house scripts used to setup and analyze simulation discussed in the aforementioned study

Directory Structure:

  • analysis_jpntbs

    • Contains saved dictionaries of residues occupancy(.json), python file containing analysis functions and jupyter notebook containing plot generation

  • fully_equil_starting_config

    Directory structure

    • BSA_DS_MR_5
      • NPT equilibration GROMACS version 2020.5 files of starting config. necessary to perform MD production run
    • BSA_SDS_MR_128
      • NPT equilibration GROMACS version 2020.5 files of starting config. necessary to perform MD production run
    • BSA_TA_MR_128
      • NPT equilibration GROMACS version 2020.5 files of starting config. necessary to perform MD production run
    • amber99sb-star-ildnp.ff
      • Protein forcefield files for GROMACS
    • setup_bash_scripts
      • Bash scripts used for simulation setup, equilibration and job submissions

  • mdp_files

    • GROMACS parameter files used for e-min, nvt and npt equilibration, scaling and production runs.

  • pdb_and_itp_files

    • Pdb and topology files for 12-mer Dextran Sulphate, Sodium Dodecyl Sulphate (SDS) and Taurocholic Acid (TA)

  • rmsd_data

    • Root mean squared deviation data of BSA backbone and its respective domains

Google drive directory with trajectory files analyzed in this study found here

Main figure generated: alt text