2020 DOCK tutorial 1 with PDBID 3VJK

Introduction

Welcome to the Rizzo lab!

This tutorial is provided by the students of stony brook to help the community better understand the DOCK toolset.

Software packages

To follow this tutorial you will need to have the following programs installed:

DOCK
sing-something

At several points this tutorial will reference these programs as commands in a shell environment. The students who did this ran their programs on a UNIX (CoreOS or Ubuntu) server, although this process should generalize to your specific setup. For help, please reference available documentation.

Sphere Selection

By this step, you should have the mol2 extractions of ligand and protein, in both hydrogenated and unhydrogenated forms (4 files). The next activity is to create an efficient representation of empty space inside the protein. This is done with the sphgen script, which tries to generate the largest possible sphere for any given empty space. In general, it is desirable for the spheres will eclipse with each other, but not with the protein itself.

The sphgen software takes in a series of inputs from prompts to the user, but we can automate this by piping these arguments through a file. We shall can this file INSPH. Generate your INSPH file with the following syntax:

   [your_receptor].dms
   <R flag> - enables sphere generation outside the protein surface (no eclipsing)
   <X flag  - uses all coordinates 
   <double> - distance that steric interactions are checked (units?)
   <double> - Maximum sphere radius of generated sphere (units?)
   <double> - Size of sphere that rolls over dms file surface for cavities (units?)
   [your_receptor].sph

This is an example of how we wrote our file:

   3vjk_receptor_woH.dms
   R 
   X 
   0.0 
   4.0 
   1.4 
   3vjk_receptor_woH.sph

Does it matter if the dms is generated with the hydrogens?

This should produce an sph file that you can then run through sphgen

sphgen -i INSPH -o OUTSPH