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: