Difference between revisions of "2022 DOCK tutorial 3 with PDBID 1X70"
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File > Fetch By Id > 1X70 | File > Fetch By Id > 1X70 | ||
| − | ==Spheres== | + | ==Surface Generation & Spheres== |
| + | This section details the generation of sphere files which will be used to describe where you are trying to DOCK to on your protein. | ||
'''Surface Generation''' | '''Surface Generation''' | ||
| + | In Chimera: | ||
| + | Load 1X70 w/o Hydrogens > actions > show > surface | ||
[[File:1X70_surface.png|thumb|center|800px|The VDW surface for 1X70 that will be used to generate the sphere files.]] | [[File:1X70_surface.png|thumb|center|800px|The VDW surface for 1X70 that will be used to generate the sphere files.]] | ||
| + | Then you will write a DMS (Molecular Surface) File | ||
| + | With the surface generated in Chimera: | ||
| + | Tools > Structure Editing > Write DMS | ||
| − | ''' | + | Now you should have a DMS file for the next step. |
| + | |||
| + | ''' Sphere Generation ''' | ||
| + | To generate spheres make the following input file: | ||
| + | "INSPH" - | ||
| + | 1X70_dms.dms #Molecular Surface File | ||
| + | R | ||
| + | X #Surface points from the DMS file to use in sphere generation ( | ||
| + | 0 #Minimum radius between spheres | ||
| + | 4.0 #Maximum radius of sphere | ||
| + | 1.4 #Minimum radius of sphere | ||
| + | 1X70_wo_H.sph #Output sphere file | ||
| + | End of File (EOF) | ||
| + | |||
| + | For more information on sphere generation see: | ||
| + | https://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm | ||
| + | |||
| + | The .sph file should give you something similar to the following image if you load it up over your protein in Chimera: | ||
[[File:1X70_spheres.png|thumb|center|800px|The spheres representing the empty space within the protein.]] | [[File:1X70_spheres.png|thumb|center|800px|The spheres representing the empty space within the protein.]] | ||
| − | + | '''Sphere Selection''' | |
| − | ''' | ||
=Making The Infamous Grid= | =Making The Infamous Grid= | ||
Revision as of 17:37, 28 February 2022
Contents
Introduction
DOCK
System Preparation
Fetching 1X70 Open Chimera: File > Fetch By Id > 1X70
Surface Generation & Spheres
This section details the generation of sphere files which will be used to describe where you are trying to DOCK to on your protein.
Surface Generation In Chimera: Load 1X70 w/o Hydrogens > actions > show > surface
Then you will write a DMS (Molecular Surface) File With the surface generated in Chimera: Tools > Structure Editing > Write DMS
Now you should have a DMS file for the next step.
Sphere Generation To generate spheres make the following input file: "INSPH" - 1X70_dms.dms #Molecular Surface File R X #Surface points from the DMS file to use in sphere generation ( 0 #Minimum radius between spheres 4.0 #Maximum radius of sphere 1.4 #Minimum radius of sphere 1X70_wo_H.sph #Output sphere file End of File (EOF)
For more information on sphere generation see: https://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm
The .sph file should give you something similar to the following image if you load it up over your protein in Chimera:
Sphere Selection
Making The Infamous Grid
Making the grid
Energy Minimization for the ligand
Docking & Virtual Screening
Rigid Docking
Fixed Anchor Docking
Flexible Docking
Placeholder
[[File:|thumb|center|800px|image placeholder]]
