2019 DOCK tutorial 1 with PDBID 2BXF
This tutorial contains a step by step approach to dock a known ligand to a known receptor.
DOCK is a molecular docking software that was originally developed at UCSF by Dr. Irwin Kuntz, Dr. Brian Shoicket, and colleagues. DOCK is used in drug discovery and molecular modeling. It consists of 2 main components: a search algorithm to explore chemical space for conformations and a scoring function to rank the results.
The tutorial will be based on the PDB file 2BXF downloaded from the PDB Database. 2BXF is the crystal structure for human serum albumin complexed with diazepam.
Organization of Directories
We set up the files in our project space as such. It will be helpful to have these folders ready ahead of time.
0.files 1.dockprep 2.surface_spheres 3.gridbox 4.dock 6.footprint 7.virtual_screen 8.virtual_screen_mpi 9.cartesianmin 10.rescore
II. Preparation of the ligand and receptor
Download the pdb file 2NNQ from PDB database save it in 0.files folder.
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 receptor
- Open the PDB file (2NNQ.pdb) via Chimera - Isolate the receptor using select tool and delete tool in Chimera. - Save the isolated receptor as a mol2 file. (2nnq_rec_noH.mol2)
- Open 2nnq_rec_noH.mol2 file again using Chimera and use the following instructions to prepare the receptor file to be used in DOCK. Tools -> Structure Editing -> Add H (To add Hydrogen atoms) Tools -> Structure Editing -> Add Charge (To add the charge use the latest AMBER force filed available for standard residues. Here we used AMBER ff14SB) Save as a mol2 file. (2nnq_rec_withH.mol2)
- If you follow the step below all the above stated steps will automatically appear one after the other to prepare the receptor. Tools -> Structure/Binding Analysis -> DockPrep
Preparation of ligand
- Open the PDB file via Chimera. - Using Chimera, isolate the ligand, add H atoms, add charge and save it as a mol2 file by following the same steps followed for the receptor.
Once all the files are prepared make sure to save the files in 1.dockprep folder.