Difference between revisions of "DOCK 3.7"

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= Tutorials =
 
= Tutorials =
These are getting quite old, need updating
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'''These are getting quite old, need updating, CUBS tutorials? New MT1 tutorial when ready'''
 
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]
 
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]
 
* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded
 
* [[DOCK 3.7 2015/04/15 abl1 Tutorial]] superseded
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= Prepare Receptor =  
 
= Prepare Receptor =  
 +
'''These scripts setup the grids and matching spheres and are used to optimize the pocket'''
 
* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands
 
* [[Protein Target Preparation]] - only beblasti and very basic blastermaster commands
 
* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster
 
* [[Protein Target Preparation Updated]] - provides an explanation of what happens during Blastermaster
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= Prepare Screening Library =
 
= Prepare Screening Library =
For new users using tldr.docking.org will be a better source for DUDE-E(Z) decoys and extrema decoys, can also do 3d building
+
'''For new users using tldr.docking.org will be a better source for DUDE-E(Z) decoys and extrema decoys, can also do 3d building'''
 
* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]
 
* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]]
 
* [[ligand preparation 3.7]]
 
* [[ligand preparation 3.7]]

Revision as of 14:48, 23 September 2020

About

DOCK 3.7 the current version in the DOCK 3 series of docking programs developed and used by the Shoichet Lab. Please read and cite the DOCK 3.7 paper Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.

DOCK 3.7 is written in Fortran and some C. It is an update of DOCK 3.6 with many improved features. DOCK 3.7 comes with all the tools necessary to prepare a protein for docking and some tools necessary to build ligands, though some tools must be obtained externally. It uses new Flexibase/DB2 files found in ZINC15. It includes tools to prepare receptors, and several auxiliary scripts.

DOCK 3.7 is available at http://dock.compbio.ucsf.edu/DOCK3.7/.

Start here

For DOCKovalent, start here

Tutorials

These are getting quite old, need updating, CUBS tutorials? New MT1 tutorial when ready

Prepare Receptor

These scripts setup the grids and matching spheres and are used to optimize the pocket

Prepare Screening Library

For new users using tldr.docking.org will be a better source for DUDE-E(Z) decoys and extrema decoys, can also do 3d building

Running Docking

Analysis

Post Docking Clustering

Post Docking Filters

Redocking with Enhanced Sampling

Rescoring

Available Libraries

Analog by Catalog

Previous verisons and compatibility

DOCK 3.7 is part of the DOCK 3 series. It differs substantially from its immediate predecessor DOCK 3.6, which uses a different format of database files that cannot be read by DOCK 3.7, and vice versa.

How to Cite

To cite the DOCK 3.7 paper, please use Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.

How to Download

DOCK 3.7 is available at http://dock.compbio.ucsf.edu/DOCK3.7/.

How to Setup a Slurm node

An example Tutorial how to setup a slurm running node can be found here: http://wiki.docking.org/index.php/Slurm

Implementation

DOCK 3.7 is written in Fortran and some C. Scripts are mostly in python and perl.

http://i.creativecommons.org/l/by-sa/3.0/88x31.png

This work is licensed under the Creative Commons Attribution-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/3.0/ This page is adapted from "DOCK3.7 Documentation" by Ryan G. Coleman. Based on a work at https://sites.google.com/site/dock37wiki/.