Revision as of 14:50, 1 March 2022

Introduction

DOCK

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

Now that we the receptor by itself, we have to clean up the rest of the receptor by adding any missing side chains, dealing with multiple occupancies and mutated residues, and protonating and calculating partial charges.

For 1X70, there are several residues with multiple occupancies.

One way to check for these residues is to grep the number of alpha carbons from the pdb in the command line.

 In the terminal, type: grep -e CA 1X70_noH.pdb

Two potential occupancies shown for CYS649

 Tools > Structure Editing > Dock Prep

Using dock prep to fill in missing atoms/sidechains, add Hydrogens and charges.

Make sure that the protonation makes sense for residues in the active site or coordinated with metals (none here), especially histidines, by checking the paper and making sure any nitrogens coordinating with metals are not protonated.

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

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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