2024 DOCK tutorial 2 with PDBID 1NDV
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Revision as of 15:40, 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
5.1
Ligand Minimization
6
Footprint Generation
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
Ligand Minimization
Footprint Generation
Rigid Docking
Fixed Anchor Docking
Flex Docking
Virtual Screening
Cartesian Minimization
reScore
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