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: 22 Apr 2025, 09:57:24
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.
Click here to open manual pages for actions used in this project.
Submission history
[v1] 06 Aug 2023: original submission
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