Andrea Basciu
Enhanced Sampling of Binding Pocket Volume and Shape (tutorial)
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)
Paper: Holo-like and Druggable Protein Conformations from Enhanced Sampling of Binding Pocket Volume and Shape
https://pubs.acs.org/doi/10.1021/acs.jcim.8b00730
Enhanced Sampling of Binding Pocket Volume and Shape (tutorial) [Part 4/4]
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
Enhanced Sampling of Binding Pocket Volume and Shape (tutorial) [Part 3/4]
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
Enhanced Sampling of Binding Pocket Volume and Shape (tutorial) [Part 2/4]
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