View source for 2015 DOCK tutorial with Poly(ADP-ribose) polymerase (PARP)

For additional Rizzo Lab tutorials see [[DOCK Tutorials]]. Use this link [http://www.mediawiki.org/wiki/Help:Formatting Wiki Formatting] as a reference for editing the wiki. This tutorial was developed collaboratively by the AMS 536 class of 2014, using DOCK v6.6.

==I. Introduction==

===DOCK===

DOCK is a molecular docking program used in drug discovery. It was developed by Irwin D. Kuntz, Jr. and colleagues at UCSF (see [http://dock.compbio.ucsf.edu/ UCSF DOCK]). This program, given a protein binding site and a small molecule, tries to predict the correct binding mode of the small molecule in the binding site, and the associated binding energy.  Small molecules with highly favorable binding energies could be new drug leads. This makes DOCK a valuable drug discovery tool. DOCK is typically used to screen massive libraries of millions of compounds against a protein to isolate potential drug leads. These leads are then further studied, and could eventually result in a new, marketable drug. DOCK works well as a screening procedure for generating leads, but is not currently as useful for optimization of those leads.

DOCK 6 uses an incremental construction algorithm called ''anchor and grow''. It is described by a three-step process:

# Rigid portion of ligand (anchor) is docked by geometric methods.
# Non-rigid segments added in layers; energy minimized.
# The resulting configurations are 'pruned' and energy re-minimized, yielding the docked configurations.

[[Image:2014_1HVR_receptor_surface.png|thumb|center|375px|1HVR Receptor surface]]

===Poly ADP Ribose Polymerase (PARP)===

'''Poly (ADP-ribose) polymerase (PARP)''' is a family of proteins involved in a number of cellular processes involving mainly DNA repair and programmed cell death. (Wikipedia: http://en.wikipedia.org/wiki/Poly_ADP_ribose_polymerase) The particular PARP family member we will focus on is PARP5b (aka: Tankyrase 2) of which the catalytic domains contains 227 amino acid residues. '''Olaparib (AZD-2281, trade name Lynparza)''' is an FDA-approved chemotherapeutic agent, developed by KuDOS Pharmaceuticals and later by AstraZeneca. It is an inhibitor of poly ADP ribose polymerase (PARP), an enzyme involved in DNA repair.[1] It acts against cancers in people with hereditary BRCA1 or BRCA2 mutations, which includes many ovarian, breast, and prostate cancers. (Wikipedia: http://en.wikipedia.org/wiki/Olaparib) 

In this class, we will perform docking experiments and virtual screening on a crystallographic structure of PARP5b in complex with a small-molecule inhibitor, olaparib (PDB ID: 4TKG).

===Organizing Directories===

While performing docking, it is convenient to adopt a standard directory structure / naming scheme, so that files are easy to find / identify. For this tutorial, we will use something similar to the following:

 ~username/AMS536/dock-tutorial/00.files/
                               /01.dockprep/
                               /02.surface-spheres/
                               /03.box-grid/
                               /04.dock/
                               /05.mini-virtual-screen/
                               /06.virtual-screen/
                              
In addition, most of the important files that are derived from the original crystal structure will be given a prefix that is the same as the PDB code, '4TKG'. The following sections in this tutorial will adhere to this directory structure/naming scheme.


==II. Preparing the Receptor and Ligand==


Matt Elmes 

Courtney Singleton 


==III. Generating Receptor Surface and Spheres==

Kellon Belfon 

Xingyu 

=== Generating the Receptor Surface ===


=== Placing Spheres ===

Sphgen is a program that generate sets of overlapping spheres that define the shape of a molecule or molecular surface. Spheres are generated over the entire receptor and ligand surface.
For further information on how Sphgen generate the spheres for receptors and ligand, please refer to the latest version of the DOCK manual:

''<http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm>''

To generate spheres using Sphgen follow the steps below:

'''Step 1.''' Create an input file name '''INSPH''' with the following information:

 vim INSPH

 4TKG.rec.dms #surface file generated above will be the input file
 R            #flag to place spheres outside (R) or inside (L) of the surface 
 X            #flag that informs sphgen of the subset of surface points to be used (X = all points)
 0.0          #flag that prevent the generation of large spheres with close surface contacts(default= 0)
 4.0          #maximum radius of the spheres generated (default = 4.0 Angstroms)
 1.4          #minimum radius of the spheres generated (default = radius of probe)
 4TKG.rec.sph #this will be the file which contained the clustered spheres generated

'''Step 2.''' Run the program Sphgen using the command sphgen:

 sphgen -i INSPH -o OUTSPH

 '''-i''' is the flag that give sphgen the input file '''INSPH''' is
 '''INSPH''' is the file created above that gives sphgen instructions
 '''-o''' is the flag to create the oputput file
 '''OUTSPH''' is the output file with the information of the spheres generated from sphgen

'''Step 3.''' Visualization of the spheres generated:

Visualization of the spheres can be done directly with '''chimera''' or with the program '''showsphere''' 

'''3 a.''' Visualization directly with '''Chimera''':

* Launch '''Chimera''', choose ''File'' -> ''Open'', choose '''4TKG.rec.sph'''

'''3 b.''' Visualization with '''showsphere''':

'''showsphere''' convert the '''.sph''' file into PDB format.

(i) Run '''showsphere''', by typing showsphere into the terminal:

 showsphere

You will be prompted with the following questions:

 Enter name of sphere cluster file:
      '''4TKG.rec.sph'''
 Enter cluster number to process (<0 = all):
      '''-1'''
 Generate surfaces as well as pdb files (<N>/Y)?
      '''N'''
 Enter name for output file prefix:
      '''output_spheres'''
 Process cluster 0 (contains ALL spheres) (<N>/Y)? 
      '''N'''

 '''-1''' is a flag that allow you to see all possible spheres

(ii) 
* Launch '''Chimera''', choose ''File'' -> ''Open'', choose '''4TKG.rec.noH.pdb'''
* Go ''File'' -> ''Open'', choose '''output_spheres.pdb''' 
You should see many spheres placed all over the receptor surface.

'''Step 4.''' Selecting spheres of interest:

==IV. Generating Box and Grid==

=== Box Generation===

* Make a new directory and name it: ''03.box-grid/''
    mkdir 03.box-grid


* Make a new file in this directory and name it ''showbox.in''
    vim showbox.in

* This will automatically open the file ''showbox.in''. Edit the file ''showbox.in'' as follows:

    Y                                               # Yes, generate a box
    8.0                                             # Size of the box in Angstroms
    ../02.surface-spheres/selected_spheres.sph      # Sphere.sph file
    1                                               # Cluster number
    4TKG.box.pdb                                    # Name of the output file


* Save the file using the command:
     :wq

* Run the command:
     showbox < showbox.in

[http://ringo.ams.sunysb.edu/images/2/2b/Box.png|111]


Cong Liu 


=== Grid computing===

==V. Docking a Single Molecule for Pose Reproduction==


Michael Cortes 

Beibei Zhang 

Prajna Shanbhogue


==VI. Virtual Screening==

george jones 

Sam Chiappone 









==VIII. Frequently Encountered Problems==