Published July 31, 2023 | Version v1
Dataset Open

MD preview for: Fighting Celiac Disease: Improvement of pH Stability of Cathepsin L In Vitro by Computational Design

Authors/Creators

  • 1. Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
  • 2. Higher Chemical College of the Russian Academy of Sciences, D. Mendeleev University of Chemical Technology of Russia

Contributors

Researcher:

  • 1. Higher Chemical College of the Russian Academy of Sciences, D. Mendeleev University of Chemical Technology of Russia

Description

Dataset structure:
This is MD preview (some initial and final files, along with light versions of principal MD trajectories) for wild-type (WT) and acidophilic mutant (V277A) cathepsin L versions. Each folder contains three variants of pH calculations:

  • pH 7
  • pH 2 (considering all ionizable residues)
  • pH 2 (considering only His 275)

See paper text for details.

Each subfolder contains seven MD-related files:

  • md.mdp: Gromacs options file
  • topol.top: system topology, including ionization states of the charged residues
  • em.gro: system coordinates before MD
  • md.gro: system coordinates after MD
  • md.tpr: Gromacs tpr file required for MD start
  • md_view.gro: system coordinates after MD without water and ions. Required for MD preview using the next trajectory file
  • md_view.xtc: "light" MD trajectory file without water and ions with coordinates saved each 100 ps (gmx trjconv "-dt 100" option). Use two latter files for MD preview in software like VMD or Pymol.

Files

README.txt

Files (251.9 MB)

Name Size Download all
md5:79930c42cb68949346a47e7c29c017ea
1.9 kB Preview Download
md5:7f382d2d87e457856fd707e8e3bc2981
251.9 MB Preview Download