DOCK 3.7: Difference between revisions
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= Topics = | = Topics = | ||
= Top level = | |||
* [[Blastermaster]] | * [[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]] | |||
== 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 == | |||
* [[mol2db2]] is the program that creates [[mol2db2 format]] database files which are read by [[DOCK 3.7]] | |||
== Molecular docking == | |||
* [[Running DOCK 3.7]] | * [[Running DOCK 3.7]] | ||
* [[INDOCK 3.7]] - file format used by [[DOCK 3.7]] | |||
== 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]] == | |||
* [[ZINC Subset DB2 file locations]] | |||
{{Template:CC-BY-SA-30}} | {{Template:CC-BY-SA-30}} | ||
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[[Category:DOCK 3.7]] | [[Category:DOCK 3.7]] | ||
[[Category:DOCK]] | [[Category:DOCK]] | ||
[[Category:Software]] | [[Category:Software]] | ||
[[Category:Internal]] | |||
Revision as of 03:54, 23 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.
Topics
Top level
- 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
- Protein Target Preparation (Adding Static Waters to the Protein Structure) (Flexible Docking)
Molecular library preparation for docking
- mol2db2 is the program that creates mol2db2 format database files which are read by DOCK 3.7
Molecular docking
- Running DOCK 3.7
- INDOCK 3.7 - file format used by DOCK 3.7
Analysis of Docking Results, including the use of decoys
- Analyzing DOCK Results
- Auto-DUD-E Test Set (external site)
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/.