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

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(→‎I. Introduction)
(→‎Organization of Directories)
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== Organization of Directories ==
 
== Organization of Directories ==
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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.
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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
 
               0.files

Revision as of 15:19, 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

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
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