2024 DOCK tutorial 2 with PDBID 1NDV
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Revision as of 15:44, 14 February 2024 by
Stonybrook
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Contents
1
Introduction
1.1
Required Software
1.2
File Set-up
2
Preparing Structure Files
2.1
Protein
2.2
Ligand
3
Surface Spheres
3.1
DMS file
3.2
sphgen
3.3
sphere selector
4
Gridbox
4.1
showbox
4.2
grid
5
Energy Minimization for Ligand
6
Footprint Generation
7
Rigid Docking
8
Fixed Anchor Docking
9
Flex Docking
10
Virtual Screening
10.1
Slurm
11
Cartesian Minimization
12
reScore
Introduction
Required Software
File Set-up
Preparing Structure Files
Protein
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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