tutorial_rdock_implementation

An implementation of rDock for CELPP using Chimera DockPrep for protein prep and RDKit for 3D ligand conformer generation.

Creation of this package was documented in the CELPPade video tutorial: https://www.youtube.com/watch?v=btf77rNU1PY

More information on CELPPade is available at the project homepage: https://github.com/drugdata/D3R/wiki/CELPPade

Usage

Building the container

Build Requirements

• Vagrant https://www.vagrantup.com/
• Virtual Box https://www.virtualbox.org/
• Binary of 64-bit Linux distribution of Chimera (tested with version 1.13) https://www.cgl.ucsf.edu/chimera

The following commands spin up a Virtual Box virtual machine via Vagrant with Singularity installed. A Makefile is then used to create the Singularity Container runnable on any machine that can run Singularity.

git clone https://github.com/drugdata/tutorial_rdock_implementation.git
cd tutorial_rdock_implementation
#
# Be sure to download 64-bit Linux version of Chimera and put binary
# in source tree directory
#
vagrant up
vagrant ssh
cd /vagrant
make singularity

Compatibility

License

See LICENSE.txt

Authors

tutorial_rdock_implementation was written by Jeff Wagner.