Difference between revisions of "DOCK 3.7"

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[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.]
  
= Topics =
+
= Highest level scripts =
 
{{TOCright}}
 
{{TOCright}}
 
= Top level =
 
 
* [[Blastermaster]] - a program prepare input for and then run [[DOCK 3.7]], a molecular docking program.
 
* [[Blastermaster]] - a program prepare input for and then run [[DOCK 3.7]], a molecular docking program.
 
* [[Ligand preparation]] - programs to create dockable databases
 
* [[Ligand preparation]] - programs to create dockable databases
  
== Protein preparation for docking ==  
+
= Protein preparation for docking =  
 
* [[Protein Target Preparation]] (Adding Static Waters to the Protein Structure) (Flexible Docking)
 
* [[Protein Target Preparation]] (Adding Static Waters to the Protein Structure) (Flexible Docking)
  
== Molecular library preparation for docking ==
+
= Molecular library preparation for docking =
 
* [[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]]
  
== Molecular docking ==
+
= Molecular docking =
 
* [[Running DOCK 3.7]]
 
* [[Running DOCK 3.7]]
 
* [[INDOCK 3.7]] - file format used by [[DOCK 3.7]]
 
* [[INDOCK 3.7]] - file format used by [[DOCK 3.7]]
  
== Analysis of Docking Results, including the use of decoys ==
+
= Analysis of Docking Results, including the use of decoys =
 
* [[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]] ==  
+
= Current cluster information pertaining to using [[DOCK 3.7]] =  
 
* [[ZINC Subset DB2 file locations]]
 
* [[ZINC Subset DB2 file locations]]
 
  
  

Revision as of 20:55, 22 February 2014

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 DOCK3.7 paper, please use Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.

Highest level scripts

  • Blastermaster - a program prepare input for and then run DOCK 3.7, a molecular docking program.
  • Ligand preparation - programs to create dockable databases

Protein preparation for docking

Molecular library preparation for docking

Molecular docking

Analysis of Docking Results, including the use of decoys

Current cluster information pertaining to using DOCK 3.7


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/.