2024 DOCK tutorial 1 with PDBID 2ITO
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Contents
- 1 Introduction
- 2 Preparation of the ligand and protein
- 3 Creating the Protein Binding Site Surface
- 4 Box and Grid Generation
- 5 Energy Minimization
- 6 DOCK
- 7 Virtual Screening of a Ligand Library
- 8 Cartesian Minimization of Virtually Screened Small Molecules
- 9 Rescoring and Ranking Virtually Screened Molecules
Introduction
For Numbered list do this:
- S
- D
- D
- P
- P
- F
These website tutorials are useful if you are unfamiliar with the following tools:
This tutorial is for PDBID 2ITO. Replace any reference to 2ITO with the protein of your choice.
Learning Objectives
These are for bullets:
- U
- G
Setting Up Your Environment
Sample picture from last year:
Downloading a protein from the PDB database
Preparation of the ligand and protein
Evaluating the Structure
Preparing the Protein file
Preparing the Ligand File
Final Steps
Creating the Protein Binding Site Surface
Creating the Required Surface (DMS) File
Generating Spheres for the Binding Site
Binding Site Spheres
Box and Grid Generation
Generating the Box
T
Generating the Grid
N
Energy Minimization
At
Ligand Minimization
Footprint Analysis
DOCK
Rigid Docking
W
Fixed Anchor Docking
T
