2025.03.24.6OIM_covalent_Steven_Pak (in progress)

DOCK6 covalent docking for pdb 6OIM

Authors: Steven Pak

Introduction

Background

DOCK6 is a molecular modeling software that can sample a molecule's geometric degrees of freedom within the context of a target binding pocket for a biomolecule, typically a protein. Today, newer methods are trying to cover different areas of chemical space. For example, de novo design philosophies generate new molecules for a target protein where molecules can be built from scratch. In this tutorial, we aim to demonstrate DOCK6's flexibility to sample molecules when they are covalently bound to the protein target. Traditionally, molecular docking assumes that molecules can be reversible inhibitors, where they interact residues, cofactors, and solvents intermolecularly. However, many market drugs can be irreversible inhibitors, where they can be directly connected to the protein

Disclaimer

While DOCK6 can automate many features. Covalent docking in DOCK6 is not an automated function. This is an involved/meticulous procedure and should be treated as such.

Methods

Preparation of files

NOTE

This step of the tutorial is arguably the most important. Please do not skip this step.

First, run this command in your work environment

wget https://raw.githubusercontent.com/tbalius/teb_docking_test_sets/main/scripts_for_tutorial/scripts_for_2023.05.08.6OIM_covalent/0001.processing.csh