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Published April 28, 2023 | Version 0.0.2
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Nano-structured Hydrotrope-Caged Cytochrome c with Boosted Stability in Harsh Environments: A Molecular Insight

  • 1. Centre for Nano and Material Sciences, Jain University, Bangalore 562112, India.
  • 2. Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland
  • 3. Institute of Plant Genetics (IPG), Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland
  • 4. International Institute of Molecular and Cell Biology in Warsaw, Ks Trojdena 4, 02-109 Warsaw, Poland

Description

The input and main output files used for the paper "Nanostructured Hydrotropes Caged Cytochrome c with Boosted Stability in Harsh Environments: A Molecular Insights" are separated in the different tar files.

Contents:

00_packmol : box built using PACKMOL package for ATP, IL and ATP_IL systems

01_Build_systems : parameters and input files for WAT, ATP, IL and ATP_IL systems

02_Minimization_Equilibration_RT : minimization and equilibration inputs, restarts and output files for WAT, ATP, IL and ATP_IL systems at 300K

03_Minimization_Equilibration_HT : minimization and equilibration inputs, restarts and output files for WAT, ATP, IL and ATP_IL systems at 363.15K

04_HTMD_Cytc_WAT_RT : HTMD input, restarts and output files for Cyt c + WAT system at 300K

05_HTMD_Cytc_ATP_RT : HTMD input, restarts and output files for Cyt c + ATP system at 300K

06_HTMD_Cytc_IL_RT : HTMD input, restarts and output files for Cyt c + IL system at 300K

07_HTMD_Cytc_ATP_IL_RT : HTMD input, restarts and output files for Cyt c + ATP_IL system at 300K

08_HTMD_Cytc_WAT_HT : HTMD input, restarts and output files for Cyt c + WAT system at 363.15K

09_HTMD_Cytc_ATP_HT : HTMD input, restarts and output files for Cyt c + ATP system at 363.15K

10_HTMD_Cytc_IL_HT : HTMD input, restarts and output files for Cyt c + IL system at 363.15K

11_HTMD_Cytc_ATP_IL_HT : HTMD input, restarts and output files for Cyt c + ATP_IL system at 363.15K

12_HTMD_MD_analysis_RT : Analysis raw data for Bayesian MSM, RDF, RMSD, RMSF, H-bonds and Secondary structure changes at 300K 

13_HTMD_MD_analysis_HT : Analysis raw data for Bayesian MSM, RDF, RMSD, RMSF, H-bonds and Secondary structure changes at 363.15K 

14_H2O_RT : Radial Distribution Function (RDF) data for simulations in explicit water and in absence of the protein Cyt c

Notes: Each folder contains INFO.md with further detailed information on respective types of data.

 

Notes

Article information: https://doi.org/10.1039/D3GC01704D

Files

Files (15.8 GB)

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md5:49a0f599fefa0cf22060b5acf2159454
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