2025 DOCK tutorial 1 with PDBID 1O86

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