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

Downloading the PDB

Having setup your necessary environment to work on seawulf, lets navigate to your local computer and begin the protein preparation process:

To begin protein preparation you will need the necessary PDB file to work with. Using this link: https://www.rcsb.org/structure/1O86, you will see the RCSB main page opened to our protein of choice:

Next, you'll want to navigate to the top right corner where it says Download Files. Then, select the dropdown arrow. The following pulldown menu will appear on the screen:

Select 'Download PDB'. Now the PDB file is downloaded to your local computer.

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Now that you have the PDB file, lets navigate to Chimera program to open the file.

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