Project ID: plumID:20.014
Name: amyloid beta small molecule interaction
Category: bio
Keywords: intrinsically disordered proteins, disordered proteins, IDPs, fuzzy binding, small molecule, drugs, entropy, binding, Alzheimer’s disease, amyloid beta
PLUMED version: 2.6.0
Contributor: Gabriella Heller
Submitted on: 08 May 2020
Last revised: 06 Nov 2020
Publication: G. T. Heller, F. A. Aprile, T. C. T. Michaels, R. Limbocker, M. Perni, F. S. Ruggeri, B. Mannini, T. Löhr, M. Bonomi, C. Camilloni, A. De Simone, I. C. Felli, R. Pierattelli, T. P. J. Knowles, C. M. Dobson, M. Vendruscolo, Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer’s disease. Science Advances. 6 (2020)

PLUMED input files

File Compatible with
PLUMED_input_files/AB42_alone/plumed/plumed.dat tested on v2.9 tested on master
…ED_input_files/AB42_and_10074_G5/plumed/plumed.dat tested on v2.9 tested on master

Last tested: 26 Feb 2024, 07:33:08

Project description and instructions
This study uses metadynamic metainference simulations restrained with NMR chemical shift data to determine the bound and unbound ensembles of a disordered peptide (amyloid beta) in the presence and absence of a small, drug-like molecule. We used PLUMED version 2.6.0 and GROMACS 2018.3.

Submission history
[v1] 08 May 2020: original submission
[v2] 06 Nov 2020: updated doi

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