2018 DOCK tutorial 1 with PDBID 2NNQ

This tutorial contains, a step by step by approach to dock a known ligand to a known receptor.

2NNQ

The tutorial will be based on the PDB file 2NNQ downloaded from the PDB Database. 2NNQ is the crystal structure for a human adipocyte fatty acid binding protein in complex with ((2'-(5-ethyl-3,4-diphenyl-1H-pyrazol-1-yl)-3-biphenylyl)oxy)acetic acid.

Organization of Directories

Maintaining a clearly organized set of folders will be helpful in finding specific files, calling different files in input files and most importantly keeping track of everything you do. We would like to recommend to maintain the following set of files throughout the tutorial.

             0.files
             1.dockprep
             2.surface_spheres
             3.gridbox
             4.
             5.
             6.
             7.

II. Preparation of the ligand and receptor

Download the pdb file 2NNQ from PDB database.

Checking the structure

 - Read the article related to the PDB file to understand protonation states, charges, environmental conditions and other important information regarding the receptor and the ligand.
 - Open the pdb file through chimera and look at the structure. Identify the main components of the model (receptor, ligand, solvent, surfactants, metal ions)
 - Carefully look to identify if there are any missing residues or missing loops. (This particular PDB file didn't contain any missing loops or missing residues)

Preparation of ligand

 - Open the PDB file via chimera.