Revision as of 10:58, 23 February 2021

Introduction

DOCK

Developed by Irwin D. Kuntz, Jr. and colleagues at UCSF, DOCK is a program used to dock molecules to one another. Docking is a process in which given a small molecule or ligand in the active site of a receptor, the program will try to predict the lowest-energy binding mode of the ligand to the receptor. This process is very important in drug discovery as small molecules that bind to or interact with the active site of a receptor associated with a disease could inhibit its function, acting as a drug. DOCK is a particularly helpful tool as it is used to screen massive libraries of molecules, containing millions of compounds, against a receptor to identify the most promising drug lead compounds.

DOCK historically used a geometric matching algorithm to superimpose the ligand onto a negative image of the active site of the receptor. Over the years, features were added that would improve the programs ability to find the lowest-energy binding mode. Somem of these features include force-field based scoring, on-the-fly optimization and an algorithm for flexible ligand docking.

In this tutorial DOCK6 will be used. New features for DOCK6 include: additional scoring options during minimization; DOCK 3.5 scoring-including Delphi electrostatics, ligand conformational entropy corrections, ligand desolvation, receptor desolvation; Hawkins-Cramer-Truhlar GB/SA solvation scoring with optional salt screening and more (see UCSF DOCK). These new features improved the programs ability to predict binding poses.

1S19

This tutorial will use PDB code: 1S19. 1S19 is the crystal structure of VDR ligand binding domain complexed to calcipotriol (find structure here. The resolution is 2.10 Å. Click Download Files -> PDB Format to download PDB file.

Chimera

UCSF Chimera was developed by Resource for Biocomputing, Visualization, and Informatics (RBVI) at the University of California, San Francisco. Chimera is a program made for the interactive visualization and analysis of molecular structures. Some features of Chimera include general structure analysis (automatic identification of an atom, hydrogen addition and partial charge assignment, structure building and bond rotation, etc.) presenting images and movies (high-res images, visual effects, standard molecular representations, etc.) and sequence structure tools (sequence alignments, structure superposition, etc.)

Making Directories

To make it easier for us to locate certain files, we are going to create directories for each step of the docking process. The mkdir command creates a new directory in which new files can be saved. The cd command allows for you to navigate between directories.

In your Bash Shell environment, create a directory containing all of the information for the project by typing:

  mkdir 1S19

To change into that directory type:

  cd 1S19

To create the directories for each step:

  mkdir 001.structure 002.surface_spheres 003.gridbox 004.dock 005.virtual_screen 006.virtual_screen_mpi 007.cartesianmin 008.rescore

To confirm that the directories have been created:

  ls

If you made a mistake and need to delete a directory:

  rm *insert name of directory to be deleted*

Preparing the Ligand and Receptor

PDB Structure

Download the structure of 1S19 from the Protein Data Bank (PDB) File:Example.jpg

Receptor

Ligand