2024 DOCK tutorial 2 with PDBID 1NDV
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Revision as of 15:39, 14 February 2024 by
Stonybrook
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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
3.1
DMS file
3.2
sphgen
3.3
sphere selector
4
Gridbox
4.1
showbox
4.2
grid
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
DMS file
sphgen
sphere selector
Gridbox
showbox
grid
Energy Minimization
Footprint
Rigid Docking
Fixed Anchor Docking
Flex Docking
Virtual Screening
Cartesian Minimization
reScore
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