Project ID: plumID:24.036
Name: Leveraging cryptic ligand envelopes through enhanced molecular simulations
Archive: https://github.com/fcolizzi/cryptic_envelope/archive/refs/heads/main.zip
Category: bio
Keywords: HREX, conformational heterogeneity, drug discovery, ligand binding, plitidepsin, aplidin, ligand-target complexes, cryptic ligand envelope
PLUMED version: 2.4
Contributor: Francesco Colizzi
Submitted on: 14 Dec 2024
Publication: unpublished

PLUMED input files

File Compatible with
2r3i/plumed.dat tested on v2.10 tested on master
2vwx/plumed.dat tested on v2.10 tested on master
5dro/plumed.dat tested on v2.10 tested on master
DIDE/plumed.dat tested on v2.10 tested on master
DIDE/plumed_water.dat tested on v2.10 tested on master
DIDE-water/plumed.dat tested on v2.10 tested on master
PLIT/plumed.dat tested on v2.10 tested on master
PLIT/plumed_h1h2.dat tested on v2.10 tested on master
PLIT/plumed_water.dat tested on v2.10 tested on master
PLIT-CH3Cl/plumed.dat tested on v2.10 tested on master
PLIT-water/plumed.dat tested on v2.10 tested on master
PLIT_A399V/plumed.dat tested on v2.10 tested on master

Last tested: 23 Apr 2025, 10:07:23

Project description and instructions
Simulations have been performed with GROMACS 2018.3 and PLUMED 2.4.3. The input files for HREX simulations of several ligand-protein complexes are provided, along with PLUMED input files for the analysis of free-in-solution and target-bound conformational heterogeneity of ligands (aka the cryptic ligand envelope).

Submission history
[v1] 14 Dec 2024: original submission

Badge
Click on the image below and get the code to add the badge to your website!
plumeDnest:24.036