Revision as of 17:45, 28 February 2022

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

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   #Whether to generate spheres outside of surface (R) or inside (L) 
 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

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:

The spheres representing the empty space within the protein.

Sphere Selection

Making The Infamous Grid

Making the grid

Energy Minimization for the ligand

Docking & Virtual Screening

Rigid Docking

Fixed Anchor Docking

Flexible Docking

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