2020 DOCK tutorial 2 with PDBID XXXX

I. Introduction

DOCKING

DOCK, a commonly used computational tool used to sample a library of small molecules, ligands and attempts to successfully dock these within their target site, typically a rigid protein into their most energetically favorable positions. To accomplish this, first DOCK uses a global search of the entire protein to determine which locations will be the most energetically favorable, which will be the anchors. Following this, these ligands will take on a variety of different geometric poses to obtain the most conformationally favorable ligand positions. This software is commonly used to perform the hit to lead process in drug discovery to narrow down the drug possibilities from up to hundreds of millions to a few hundred. The drug discovery process then continues using this framework to further select and refine the potential drug candidates.

2GQG

This rigid protein is of the ABL Kinase Domain with the ligand being Dasatinib. This structure was identified using X-ray crystallography with a 2.4A resolution, lower resolutions are preferred.

Directories

For this part of the experiment, create an initial directory in your linux operating systems to work on your experiment

          mkdir 2GQG_Experiment

Following this change the directory to this directory

          cd 2GQG_Experiment

Use the mkdir command in your linux operating system to make all these directories to store your files for the experiment

          00.files
          01.dock_prep
          02.surface_spheres
          03.grid_box
          04.dock
          05.footprint
          06.virtual_screen
          07.virtual_screen_mpi
          08.cartesian_min
          09.rescore

II. Protein and Ligand Preparation

For the first step open up your chimera, go to file and fetch by ID to retrieve the PDB file 2GQG.

The Kinase is dimerized with another kinase to form 2 different chains so delete one of these chains. To produce the resulting image shown in Figure 1.

Check the structure

Read over the information for this protein-ligand complex to determine the charge and environment of the structure to make sure everything is correct. Make sure that there are no issues with the molecules, that aren't physically possible because otherwise they do not accurately represent the experimentally known.

Receptor Preparation

Open up the 2GQG.pdb file, Delete all non standard residues in the structures including the solvent molecules, water and the ligand. To do this task, go in chimera to select->residue->all-nonstd atoms. Following this delete these molecules.

Unique features specifically to this receptor, Delete the Phosphorous atom from this file because it isn't close to the docking site and this phosphorous atom is significantly difficult to parameterize. Also swap two of the residues in the protein structure, the PTR residue on residue 172 with TYR and the ARG residue on 164 with another ARG. To swap these residues, change these residue structures

Use this command line to switch the residue. This swaps the current 172 residue on chain a with tyr. Use this same command to swap the argine residues.

swapaa tyr :172.a

Delete all the H's remaining on the receptor using the chimera database select->chemistry->elements->H. Then delete using the Actions->Atoms/bonds->delete command. Save this receptor as 2GQG_receptor_noH.mol2 using the command File->save mol2

Using the 2GQG_receptor_noH.mol2 add H's to the receptor with the command tools->structural editing->add H. Following this add amber charges to the molecule using the command tools-> structural editing-> add charge. The charge you should add are AM1BCC charges to the residues. Without these charges the coulomb's interaction wouldn't be calculated in the docking software.

Save the receptor as 2GQG_receptor_wH.mol2

Ligand Preparation

Open up the original PDB file in chimera, identify which nonstandard reside is the ligand using the select->residues->nonstd amino acid. Once the ligand has been selected use the inverted selected models select->invert(selected models) to select everything besides the ligand and delete these structures.

Add the hydrogens and AM1BCC charges to the ligand structure. Save this structure as 2GQG_ligand_wH.mol2

Add all these files into the 01.dock_prep directory

II. Generating Surface and Spheres

The purpose of this part is determine the anchor positions on the protein which is where the ligands will grow from.

Prep DMS Files

open up the 2GQG_receptor_noH.mol2 within Chimera, make sure to use the receptor file with no H.

First generate all the spheres necessary using action-> surface -> show

Save this sphere file into a DMS file using the command Tools-> Structural Editing -> Write DMS and save as 2GQG_receptor_noH.dms

Generating Spheres

change directories into the 03.surface_spheres directory

      cd 03.surface_spheres

Create a new file titled INSPH using the vim command in linux, then type the following into the INSPH file

      vim INSPH

This file generates all the spheres that are capable of occupying the protein

2GQG_receptor_noH.dms
R
X
0.0
4.0
1.4
2GQG_receptor_noH.sph

==Sphere Selector

This part is

sphgen -i INSPH -o OUTSPH

This will selectively choose the spheres in the sphere file previously made and choose the spheres less than 10.0 angstroms. The purpose of this part is to narrow the docking process by choosing only the places that are in the binding pocket of the ligand. If this search isn't performed the dock search would run docking simulations attempting to dock the ligand into unfavorable binding sites.

sphere_selector 2GQG_receptor_noH.sph ../01.dock_prep/2GQG_ligand_wH.mol2