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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Having setup your necessary environment to work on seawulf, lets navigate to your local computer and begin | Having setup your necessary environment to work on seawulf, lets navigate to your local computer and begin | ||
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Next, you'll want to navigate to the top right corner where it says Download Files. Then, select the dropdown arrow. | 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: | The following pulldown menu will appear on the screen: | ||
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[[File:1O86_RCSB_2.png]] | [[File:1O86_RCSB_2.png]] | ||
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| + | Select 'Download PDB'. Now the PDB file is downloaded to your local computer. | ||
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| + | ---- | ||
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| + | Now that you have the PDB file, lets navigate to Chimera program to open the file. | ||
== 002: Spheres == | == 002: Spheres == | ||
Revision as of 16:29, 18 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
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.
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
