Project ID: plumID:23.046
Name: Lasso Peptides - HLDA CV
Archive: https://github.com/gabedahora/HLDA-WTMetaD-lasso/raw/main/lasso_HLDA.zip
Category: bio
Keywords: metadynamics, protein folding, HLDA, harmonic
PLUMED version: 2.7.1
Contributor: Gabriel da Hora
Submitted on: 21 Dec 2023
Publication: G. C. A. da Hora, M. Oh, J. D. M. Nguyen, J. M. J. Swanson, One Descriptor to Fold Them All: Harnessing Intuition and Machine Learning to Identify Transferable Lasso Peptide Reaction Coordinates. The Journal of Physical Chemistry B (2024)
PLUMED input files
| File | Compatible with |
|---|---|
| github/MccJ25/plumed.dat |   |
| github/Sun/plumed.dat | |
| github/Uln/plumed.dat | |
Last tested: 22 Apr 2024, 20:41:45
Project description and instructions
These are AMBER and PLUMED files to run Well-Tempered Metadynamics for each lasso peptide (MccJ25, ulleungdin and sungsanpin) with two CVs. One of the CVs biases the isopeptide bond between residues 1 and 8 and the second is defined by HLDA as a combination of weighted distances from the ring 1-8 to the piercing residue.
Submission history
[v1] 21 Dec 2023: original submission
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