Difference between revisions of "2025 DOCK tutorial 1 with PDBID 1O86"
Stonybrook (talk | contribs) (→000: Foundations) |
Stonybrook (talk | contribs) (→001: Structure Prep) |
||
| Line 16: | Line 16: | ||
To begin protein preparation you will need the necessary PDB file to work with. Using this link: https://www.rcsb.org/structure/1O86, | 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: | you will see the RCSB main page opened to our protein of choice: | ||
| + | |||
| + | [[File:RCSB.png]] | ||
== 002: Spheres == | == 002: Spheres == | ||
Revision as of 16:11, 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
Protein Preparation
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:
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
