Difference between revisions of "DOCK 3.7"

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= About =  
 
= About =  
DOCK 3.7 is available at  [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].
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It is the latest version in the [[DOCK 3]] series of docking programs developed and used by the [[Shoichet Lab]]. To cite the DOCK 3.7 paper, please use
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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
 
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]
 
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 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  
 
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, written in a variety of languages. It comes with some tools necessary to build ligands, though some tools are under commercial/free academic
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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.
license that must be obtained externally. It uses new Flexibase/DB2 files found on ZINC (eventually). It includes tools to prepare receptors,
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written in a variety of languages, and several auxiliary scripts written in Python.
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DOCK 3.7 is available at  [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].
 +
 
 
{{TOCright}}
 
{{TOCright}}
  
 
= Start here =
 
= Start here =
* [[So you want to set up a lab]]
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* [[So you want to set up a lab]] - only if you don't already have hardware ready.
 
* [[Install DOCK 3.7]]
 
* [[Install DOCK 3.7]]
 
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]
 
* [[DOCK 3.7 2014/09/25 FXa Tutorial]]
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= Available Libraries =  
 
= Available Libraries =  
 
* [[ZINC Subset DB2 file locations]]
 
* [[ZINC Subset DB2 file locations]]
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* how to get db2 files from zinc15.docking.org
  
= Previous verisons =  
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= Previous verisons and compatibility =  
DOCK 3.7 is part of the [[DOCK 3]] series. However, it differs substantially from its immediate predecessor [[DOCK 3.6]].  Importantly, [[DOCK 3.6]] uses a different format of database files that cannot be read by [[DOCK 3.7]] and vice versa.  
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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 =  
 
= How to Cite =  
Line 54: Line 58:
 
DOCK 3.7 is available at  [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].
 
DOCK 3.7 is available at  [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].
  
= Programming Language =  
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= Implementation =  
DOCK 3.7 is written in Fortran and some C. Scripts are mostly in [[python]] and perl.  
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DOCK 3.7 is written in Fortran and some C. Scripts are mostly in [[python]] and [[perl]].
  
 
{{Template:CC-BY-SA-30}}
 
{{Template:CC-BY-SA-30}}

Revision as of 23:35, 2 June 2015

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

Prepare Receptor

Prepare Screening Library

Running Docking

Analysis

Available Libraries

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/.

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/.