2022 DOCK tutorial 3 with PDBID 1X70

System Preparation

Fetching 1X70

Open Chimera and do the following to grab the protein:

File > Fetch By ID > 1X70

Biological assembly 1 of 1X70.

The first thing to notice is that this is a dimer and the ligand, 715, is not bound at the dimer interface. Thus, one of the monomers is entirely redundant and should be deleted.

Select > Chain > A

Actions > Atoms > Delete

Next it is important to remove cofactors, ions, and water molecules not involved in the binding interactions. This can be checked by reading through the paper associated with the PDB.

Select > Residue > NAG > Actions > Atoms > Delete

Select > Residue > NDG > Actions > Atoms > Delete

Select > Residue > HOH > Actions > Atoms > Delete

This will leave us with just the ligand and receptor.

1 monomer of 1X70 with all waters and non standard residues deleted except for the ligand 715, which is colored light blue for clarity.

Receptor Prep

Receptor 1X70 without Hydrogens

Ligand Prep

715 without Hydrogens added

715 with Hydrogens

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

Energy Minimization for the ligand

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Docking & Virtual Screening

Rigid Docking

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Fixed Anchor Docking

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Flexible Docking

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