| Molecular Modeling Lab |
EDES project
In this page you can find the Enhanced Sampling of Binding and Pocket Volume and Shape (EDES) tutorial. We will exploit enhanced-sampling molecular dynamics, namely metadynamics, to improve the sampling of bound-like (holo)
https://pubs.acs.org/doi/10.1021/acs.jcim.8b00730
Go to the THIRD part of the Tutorial Analyzing the metadynamics simulation In this section, we are going to evaluate the enhancement of "breathing motions" of the BS (in terms of RoG oscillations,
Go to the SECOND part of the Tutorial Go to the FOURTH part of the Tutorial Preparing the PLUMED input files In the previous section you edited the plumed-common.dat file containing the
Go to the FIRST part of the Tutorial Go to the THIRD part of the Tutorial A brief recap on Metadynamics (safely skip this section if you are familiar with the method) We
Introduction In this tutorial we will exploit enhanced sampling molecular dynamics (MD), namely metadynamics [1], to improve the sampling of bound-like (holo) conformations of a protein starting from its unbound (apo) one. This