Project ID: plumID:22.007
Name: Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy
Archive: https://github.com/ELELAB/LC3C_NDP52_GE_mutant/raw/master/plumednest/plumednest.zip
Category: bio
Keywords: metadynamics, well-tempered, protein-protein interactions, disordered proteins, mutations autophagy
PLUMED version: 2.5.3
Contributor: Elena Papaleo
Submitted on: 08 Feb 2022
Last revised: 09 Feb 2022
Publication: A. Di Rita, D. F. Angelini, T. Maiorino, V. Caputo, R. Cascella, M. Kumar, M. Tiberti, M. Lambrughi, N. Wesch, F. Löhr, V. Dötsch, M. Carinci, P. D’Acunzo, V. Chiurchiù, E. Papaleo, V. V. Rogov, E. Giardina, L. Battistini, F. Strappazzon, Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy. Cell Death & Differentiation. 28, 2499–2516 (2021)
PLUMED input files
| File | Compatible with |
|---|---|
| metad_wte/plumed.dat |   |
Last tested: 22 Apr 2025, 10:00:44
Project description and instructions
We included the files to reproduce the metaD simulations associated with this paper. We included the files to reproduce the WT-metaD simulation with the CHARMM22star and TIPS3P water model. We provide the input files for the metaD simulation (plumed.dat reference.pdb sim.tpr). We performed the simulations using GROMACS 2019.4 and PLUMED 2.5.3. The corresponding trajectories are deposited here.
Click here to open manual pages for actions used in this project.
Submission history
[v1] 08 Feb 2022: original submission
[v2] 09 Feb 2022: update doi
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