PLUMED-NEST

Project ID: plumID:23.019
Name: Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors
Archive: https://github.com/raitis-b/plumed_nest/raw/b1c67e3fd73a70885889f6220a5959199b3a8f08/plm_path_sketchmap.zip
Category: bio
Keywords: binding pathway, binding energy, sketch-map, drug development
PLUMED version: 2.7.2
Contributor: Raitis Bobrovs
Submitted on: 24 May 2023
Publication: R. Bobrovs, L. Drunka, I. Kanepe, A. Jirgensons, A. Caflisch, M. Salvalaglio, K. Jaudzems, Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors. Journal of Chemical Information and Modeling. 63, 6890–6899 (2023)

PLUMED input files

File	Compatible with
plm_path_sketchmap/path/plumed.dat
…_sketchmap/sketch-map/plumed_for_reference_map.dat
…etchmap/sketch-map/plumed_map_to_reference_map.dat
plm_path_sketchmap/sketch-map/plumed_sketchmap.dat

Last tested: 22 Apr 2024, 20:42:40

Project description and instructions
Input structure and plumed files for sampling the inhibitor binding to Malaria aspartic protease using path metadynamics. Simulations were run using GROMACS2021 patched with PLUMED2.7. Sketchmap analysis was performed using PLUMED development version 2.8.0-dev (03.2023).

Submission history
[v1] 24 May 2023: original submission

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