The tutorial will show you how to use ProCare to align protein cavities. A cavity is described as point clouds in which each point has a pharmacophoric property [J. Desaphy et al. J. Chem. Inf. Model., vol. 52, no 8, p. 2287‑2299 (2012)]. ProCare aligns two point clouds using a Point Cloud Registration algorithm allowing the comparison of cavities of different size (local alignment) [M. Eguida et al. J. Med. Chem., vol. 63, no 13, p. 7127‑7142 (2020)]. In this tutorial, co-crystallized fragmented ligands from the Protein Data Bank will be aligned onto the cavity of a target protein to suggest seed fragments for the de novo construction of a ligand.
Material
The complete tutorial material can be downloaded here :
https://drugdesign.unistra.fr/CS3/2022
NB : The exercise will be done on your personal computer. To speed up preparation time, please install all necessary software BEFORE the session begins.
Installation
The ProCare software runs only on Linux operating systems. If you use another operating system, it is possible to run ProCare using virtualization software.
Linux
First download the “CS3_2022_procare.zip” archive and unzip it. Then follow the instructions given in the output directory to install software and scripts. Be careful ! 7 Gb of free space is required !
MacOS or Windows
You will need the VirtualBox software installed on your computer. You can download this software by clicking on the corresponding link :
- Windows : https://download.virtualbox.org/virtualbox/6.1.34/VirtualBox-6.1.34a-150636-Win.exe
- MacOS : https://download.virtualbox.org/virtualbox/6.1.34/VirtualBox-6.1.34-150636-OSX.dmg
NB1 : It is possible to use VMware software for this tutorial if you already installed it.
NB2 : For Mac users, VirtualBox must has permission to access the computer. After installation, go to the Security and Privacy panel to change the security rule.
Then download the “Ubuntu_CS3_2022.zip” archive and unzip it. Be careful ! 14 Gb of free space is required ! The output directory contains the virtual machine file named “Ubuntu_CS3_2022.vmdk” in which there is an Ubuntu distribution with everything already installed.
To login use the following credentials :
- username : puser
- password : 1234