Difference between revisions of "2025 DOCK tutorial 1 with PDBID 1O86"

Revision as of 13:22, 19 February 2025

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

Generate the required surface file

1. Open 1O86 protein only file in chimera and hit select > show> surface 2. Write the DMS file by choosing tools>structure editing>Write DMS 3. Upload the DMS file to your directory 4. Create a sphere input file using the following command:

vi INSPH

5. Paste the following into your input file:

./IO86.dms
R
X
0.0
4.0
1.4
IO86.sph

6. Run the program with the following command

sphgen -i INSPH -o OUTSPH

7. Download the output file to your local directory and open and overlay with protein file in Chimera File:Screenshot 2025-02-19 130820.png

Based on the overlay the ribbons are aligned with the spheres indicating the generation of surface spheres was successful.

Generate Spheres localized on binding site

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