Difference between revisions of "DOCK 3.7"

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* [[DOCK 3.7 Development]] - for software developers
 
* [[DOCK 3.7 Development]] - for software developers
  
= Protein preparation for docking =  
+
= Prepare Receptor =  
 
* [[Protein Target Preparation]]
 
* [[Protein Target Preparation]]
 
** [[Adding Static Waters to the Protein Structure]]
 
** [[Adding Static Waters to the Protein Structure]]
 
** [[Flexible Docking]]
 
** [[Flexible Docking]]
  
= Molecular library preparation for docking =
+
= Prepare Screening Library =
 
* [[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]]
  
= Molecular docking =
+
= Running Docking =
 
* [[Running docking 3.7]] - JJI currently working on this.
 
* [[Running docking 3.7]] - JJI currently working on this.
 
* [[Running DOCK 3.7]] - this seems to be slightly dated.
 
* [[Running DOCK 3.7]] - this seems to be slightly dated.
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* Interpreting the [[OUTDOCK 3.7]] file.
 
* Interpreting the [[OUTDOCK 3.7]] file.
  
= Analysis of Docking Results, including the use of decoys =
+
= Analysis =
 
* [[Analyzing DOCK Results]]
 
* [[Analyzing DOCK Results]]
 
* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site)  
 
* [http://autodude.docking.org/ Auto-DUD-E Test Set] (external site)  
  
= Current cluster information pertaining to using [[DOCK 3.7]] =  
+
= Available Libraries =  
 
* [[ZINC Subset DB2 file locations]]
 
* [[ZINC Subset DB2 file locations]]
  
 
= Previous verisons =  
 
= Previous verisons =  
 
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.  
 
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.  
 +
 +
= How to Cite =
 +
To cite the DOCK 3.7 paper, please use
 +
[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075992 Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.]
 +
 +
= How to Download =
 +
DOCK 3.7 is available at  [http://dock.compbio.ucsf.edu/DOCK3.7/ http://dock.compbio.ucsf.edu/DOCK3.7/].
 +
 +
= Programming Language =
 +
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 07:43, 14 March 2014

About

DOCK 3.7 is available at http://dock.compbio.ucsf.edu/DOCK3.7/. 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 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, written in a variety of languages. It comes with some tools necessary to build ligands, though some tools are under commercial/free academi c license that must be obtained externally. It uses new Flexibase/DB2 files found on ZINC (eventually). It includes tools to prepare receptors, written in a variety of languages, and several auxillary scripts written in Python.

Start here

Prepare Receptor

Prepare Screening Library

Running Docking

Analysis

Available Libraries

Previous verisons

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.

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/.

Programming Language

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/.