Difference between revisions of "2024 DOCK tutorial 2 with PDBID 1NDV"

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(Analyzing the Protein Structure:)
(Introduction)
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== Introduction ==
 
== Introduction ==
=== Required Software ===
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DOCK is a powerful computational tool
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=== Required Software and Skills ===
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In order to complete this tutorial [https://www.cgl.ucsf.edu/chimera/download.html 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 [https://ringo.ams.stonybrook.edu/index.php/Chimera tutorial] for a more in depth guide on the program.
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It is also recommended that you have experience with Unix and vi. A Unix tutorial can be found on the site [https://ringo.ams.stonybrook.edu/index.php/Unix here] and a vi tutorial can be found [https://ringo.ams.stonybrook.edu/index.php/Vi here].
 
=== File Set-up ===
 
=== File Set-up ===
  

Revision as of 11:47, 16 March 2024

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.

1ndv raw pdb.jpg

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.


1ndv coordination.jpg

Ligand

Surface Spheres

DMS file

sphgen

sphere selector

Gridbox

showbox

grid

Energy Minimization for Ligand

Footprint Generation

Rigid Docking

Fixed Anchor Docking

Flex Docking

Virtual Screening

Slurm

Cartesian Minimization

reScore