Project ID: plumID:23.031
Name: Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN
Archive: https://github.com/COSBlab/SHAMAN-benchmark/raw/main/SHAMAN-benchmark.zip
Category: bio
Keywords: RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites
PLUMED version: 2.10
Contributor: Max Bonomi
Submitted on: 06 Aug 2023
Publication: F. P. Panei, P. Gkeka, M. Bonomi, Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN. Nature Communications. 15 (2024)
PLUMED input files
Last tested: 23 Apr 2025, 10:10:09
Project description and instructions
PLUMED input files to perform Shadow Mixed-Solvent MetaDynamics simulations. Simulations have been performed with the master branch of PLUMED available here and GROMACS 2021.5. All the GROMACS topology files are available here.
Submission history
[v1] 06 Aug 2023: original submission
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