2023 DOCK tutorial 1 with PDBID 4S0V

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This tutorial teaches you how to dock a drug molecule to a receptor.

Introduction

DOCK

Virtual Screening

Directory layout

PDB #4S0V Details

Preparation of the ligand and protein

Evaluating the Structure

Preparing the Protein file

Preparing the Ligand File

Checking Hydrogen Atoms and Atom Charges

Creating the Protein Binding Site Surface

Creating the Required Surface (DMS) File

Generating Spheres for the Binding Site

Selecting the Appropriate Spheres

Generating the Required Box and Grid

Generating the Box

Generating the Grid

Docking

Energy Minimization Steps

Footprint Analysis

Rigid Docking

Fixed Anchor Docking

Flexible Docking

Virtual Screening a Library of Available Ligands

Virtual Screeni mpi

Virtual Screening Output

Cartesian Minimization

Docked Molecules Rescoring

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