2024 DOCK tutorial 2 with PDBID 1NDV

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Introduction

Required Software

File Set-up

Preparing Structure Files

Protein

Caption

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

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