2024 DOCK tutorial 2 with PDBID 1NDV
Contents
Introduction
DOCK is a powerful computational tool
Required Software and Skills
In order to complete this tutorial UCSF Chimera is required. Chimera is a powerful visualization tool that will aid in the preparation and analysis of the virtual screen. Please note that the newer version, Chimera X, can not be used for this tutorial as it lacks certain integrations with DOCK. While this tutorial will walk you through all steps necessary to use Chimera, it may be helpful to view this tutorial for a more in depth guide on the program.
It is also recommended that you have experience with Unix and vi. A Unix tutorial can be found on the site here and a vi tutorial can be found here.
File Set-up
Preparing Structure Files
Protein
Analyzing the Protein Structure:
Open your protein.pdb in Chimera.
Assess the protein structure:
1. Are there any missing loops?
2. Are there any metal coordination atoms forming key interactions with the protein?
The .pdb for 1ndv from the RCSB Protein Data Bank is shown below.
Assessment:
1. No missing loops.
2. Zinc coordination with the protein and a water molecule. This zinc atom must be kept in the protein prep.
