Published September 8, 2023
| Version v1
Dataset
Open
Unveiling the Catalytic Mechanism of NADP+-Dependent Isocitrate Dehydrogenase with QM/MM Calculations
Authors/Creators
- 1. LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da, Universidade do Porto
Description
Raw molecular dynamics simulations for the complexes simulated for 20 ns with the AMBER 12 software. Details can be found in the original manuscript (https://doi.org/10.1021/acscatal.5b01928). Molecular topology in AMBER Parameter Topology format and Trajectories in NETCDF binary coordinate format.
Two protonation states were simulated: non-charged state of catalytic Lys212/Asp275 (LYN626+ASH275+ASP666) and charged state of catalytic Lys212/Asp275 (LYS626+ASP275+ASP666)
Production trajectories are included in the MM-MD folders. Input and restart coordinates files for reproducibility are located in folders inputs and rst.
Instructions for the calculations are summarized in amber_min-md.sh.
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Related works
- Is source of
- Journal article: 10.1021/acscatal.5b01928 (DOI)