Difference between revisions of "2025 DOCK tutorial 1 with PDBID 1O86"
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Download PDB, separate lig/rec, model loops, addH/charge | Download PDB, separate lig/rec, model loops, addH/charge | ||
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surface generation, sphgen, selecting spheres, visualization in Chimera | surface generation, sphgen, selecting spheres, visualization in Chimera | ||
Revision as of 20:04, 17 February 2025
Contents
DOCK Tutorial using PDB 1O86
[intro text]
000: Foundations
Directory setup, copying files to Seawulf, Chimera, basic Unix commands
001: Structure Prep
Download PDB, separate lig/rec, model loops, addH/charge
002: Spheres
surface generation, sphgen, selecting spheres, visualization in Chimera
003: Grid/box
showbox, grid generation, visualization in Chimera
004: Minimization
Explanation of .in file for minimization and process (Chimera visuals after)
005: Rigid Docking
Explanation of .in file for rigid docking and process (Chimera visuals after)
006: Flexible Docking
Explanation of .in for flex docking (Chimera visuals after)
007: Footprint Scoring
Explanation of .in for FPS, use of Python script to generate graph
008: 5k Virtual Screen
Slurm and queue etiquette, VS .in explanation and queue submission, ViewDock in Chimera
