Dock Campaign Template

An opinionated template for a Dock based virtual screening campaign

• Dock involves running a bunch of fortran wrapped in python wrapped in shell scripts. This template setups a standard way to organize the data and common workflows.

• For each call to a script in scripts/, I recommand reading through it to make sure you understand what it is doing.

• All files/folders with date codes indicate that once the analysis is done they are immutable, and can be referenced externally. To keep sortable I like to use the format YYYYMMDD.

• For scripts that must be run sequentially number them with leading 0s so they are sortable

Getting started

0. Install DOCK (http://dock.compbio.ucsf.edu/)

   0. Go to click on DOCK 3
   1. Click the Obtaining Dock -> License Information link
   2. Click either link for academic license or follow instructions for the industry license.
   3. Specify version Dock 3.8
   4. Submit and wait for the email/download link

1. Clone the template repo to somewhere you can reference. I like to put it in ~/opt/dock_campaign_template.git

cd ~/opt
git clone https://github.com/maomlab/dock_campaign_template.git

2. Create a base directory for the project, e.g. for example for docking to KCNQ channels on the UMich Great Lakes cluster we may use ~/turbo/KCNQ/docking

cd ~/turbo/KCNQ
mkdir docking
cd docking


2. Initialize the environment. Currently this is setup up for paths on the bkslab cluster, so modify for your environment. This creates several directories.
```shell
source ~/opt/dock_campaign_template/scripts/initialize_dock_campaign.sh

3. Edit setup_dock_environment.sh for your environment. For example if you can submit jobs to a HPC cluster, fill in the cluster type and parameters

Using the Dock Campaing Template

Each time you log in, source the setup file to set paths etc.

source setup_dock_environment.sh

Docking involves a series of stages from setting up the receptor and database to running dock

At each stage call the wizard to guide you through using the templates

${DOCK_TEMPLATE}/scripts/wizard.sh