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).

Generate an INSPH file with the following syntax:

   [your_receptor].dms
   <R flag> - enables sphere generation outside the protein surface
   <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?