PyRod is a python-based library to generate three-dimensional pharmacophore models based on water traces of molecular dynamics simulations. The article describes a workflow using PyRod to generate pharmacophores for virtual screening. Nevertheless, the proposed protocol requires the use of different software including commercial one such as Ligand Scout
Schaller, David, Szymon Pach, Marcel Bermudez, and Gerhard Wolber. “Protein-Ligand Interactions and Drug Design.” Methods in Molecular Biology 2266 (2021): 227–38.
PyRod is a python-based library to generate three-dimensional pharmacophore models based on water traces of molecular dynamics simulations. The article describes a workflow using PyRod to generate pharmacophores for virtual screening. Nevertheless, the proposed protocol requires the use of different software including commercial one such as Ligand Scout