Difference between revisions of "2019 DOCK tutorial 1 with PDBID 2BXF"

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(→‎I. Introduction)
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===DOCK===
 
===DOCK===
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DOCK is a molecular docking program used in drug discovery and molecular modeling. It was developed at UCSF by Dr. Irwin D. Kuntz, Jr. and colleagues at UCSF (see [http://dock.compbio.ucsf.edu/ UCSF DOCK]). This program, given a protein binding site and a small molecule, tries to predict the correct binding mode of the small molecule in the binding site, and the associated binding energy.  Small molecules with highly favorable binding energies could be new drug leads. This makes DOCK a valuable drug discovery tool. DOCK is typically used to screen massive libraries of millions of compounds against a protein to isolate potential drug leads. These leads are then further studied, and could eventually result in a new, marketable drug. DOCK works well as a screening procedure for generating leads, but is not currently as useful for optimization of those leads.
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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.
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DOCK 6 uses an incremental construction algorithm called ''anchor and grow''. It is described by a three-step process:
 
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# Rigid portion of ligand (anchor) is docked by geometric methods.
 
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# Non-rigid segments added in layers; energy minimized.
 
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# The resulting configurations are 'pruned' and energy re-minimized, yielding the docked configurations.
 
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===2BXF===
 
===2BXF===
 
The tutorial will be based on the PDB file 2BXF downloaded from the PDB Database.
 
The tutorial will be based on the PDB file 2BXF downloaded from the PDB Database.
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2BXF is the crystal structure for  
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2BXF is the crystal structure for human serum albumin complexed with diazepam.
  
 
== Organization of Directories ==
 
== Organization of Directories ==
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               3.gridbox
 
               3.gridbox
 
               4.dock
 
               4.dock
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              5.
 
 
               6.footprint
 
               6.footprint
 
               7.virtual_screen
 
               7.virtual_screen

Revision as of 15:16, 11 February 2019

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

I. Introduction

DOCK

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.

2BXF

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

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.dock
             6.footprint
             7.virtual_screen
             8.virtual_screen_mpi
             9.cartesianmin
             10.rescore
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