2024 DOCK tutorial 2 with PDBID 1NDV

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Contents

1 Introduction
- 1.1 File Set-up
2 Preparing Structure Files
- 2.1 Protein
- 2.2 Ligand
3 Surface Spheres
4 Gridbox
5 Energy Minimization
6 Footprint
7 Rigid Docking
8 Fixed Anchor Docking
9 Flex Docking
10 Virtual Screening
11 Cartesian Minimization
12 reScore

Introduction

File Set-up

Preparing Structure Files

Protein

Ligand

Surface Spheres

Gridbox

Energy Minimization

Footprint

Rigid Docking

Fixed Anchor Docking

Flex Docking

Virtual Screening

Cartesian Minimization

reScore

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