Difference between revisions of "2024 DOCK tutorial 2 with PDBID 1NDV"
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== Introduction == | == Introduction == | ||
| − | DOCK is a powerful computational tool used in drug design. "Docking" refers to the identification of low energy binding conformations of a small molecule, or ligand, in an active site. There are three methods in which DOCK performs docking: rigid, fixed anchor, and flexible. DOCK also has the ability to perform a virtual screen, which is analogous to a high throughput screen often performed in wet labs. This method allows for thousands of molecules to be docked and ranked so that the highest scoring molecules can move to the next stage of testing. A virtual screen can save both time and money when compared to a traditional high throughput screen. This tutorial will guide you through the process of performing each method of docking, a virtual screen, and associated analysis. | + | DOCK is a powerful computational tool used in drug design. "Docking" refers to the identification of low energy binding conformations of a small molecule, or ligand, in an active site. There are three methods in which DOCK performs docking: rigid, fixed anchor, and flexible. DOCK also has the ability to perform a virtual screen, which is analogous to a high throughput screen often performed in wet labs. This method allows for thousands of molecules to be docked and ranked so that the highest scoring molecules can move to the next stage of testing. A virtual screen can save both time and money when compared to a traditional high throughput screen. This tutorial will guide you through the process of performing each method of docking, a virtual screen, and associated analysis using PDB 1NDV. |
=== Required Software and Skills === | === Required Software and Skills === | ||
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. | 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. | ||
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]. | 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]. | ||
| − | === | + | === Set-up === |
| + | Before we begin, we need to set up our directories and download our file from the Protein Data Bank (PDB) | ||
| + | ===== Downloading PDB 1NDV ===== | ||
== Preparing Structure Files == | == Preparing Structure Files == | ||
Revision as of 13:07, 16 March 2024
Contents
Introduction
DOCK is a powerful computational tool used in drug design. "Docking" refers to the identification of low energy binding conformations of a small molecule, or ligand, in an active site. There are three methods in which DOCK performs docking: rigid, fixed anchor, and flexible. DOCK also has the ability to perform a virtual screen, which is analogous to a high throughput screen often performed in wet labs. This method allows for thousands of molecules to be docked and ranked so that the highest scoring molecules can move to the next stage of testing. A virtual screen can save both time and money when compared to a traditional high throughput screen. This tutorial will guide you through the process of performing each method of docking, a virtual screen, and associated analysis using PDB 1NDV.
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.
Set-up
Before we begin, we need to set up our directories and download our file from the Protein Data Bank (PDB)
Downloading PDB 1NDV
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.
