DOCK 3.7: Difference between revisions
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* [[So you want to set up a lab]] | |||
* [[Install DOCK 3.7]] | |||
* [[Getting started with DOCK_3.7]] - notes by JJI, work in progress. | * [[Getting started with DOCK_3.7]] - notes by JJI, work in progress. | ||
* [[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. | ||
Revision as of 07:41, 13 March 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 the DOCK 3.7 paper, please use Coleman, Carchia, Sterling, Irwin & Shoichet, PLOS ONE 2013.
Start here
- So you want to set up a lab
- Install DOCK 3.7
- Getting started with DOCK_3.7 - notes by JJI, work in progress.
- Blastermaster - a program prepare input for and then run DOCK 3.7, a molecular docking program.
- Ligand preparation 3.7 - programs to create dockable databases
- Ligand preparation - somewhat different, apparently refers to versions on the UCSF/Toronto clusters, not in the distribution.
- Running docking 3.7 - how to actually run docking.
Protein 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
- ligand preparation 3.7
Molecular docking
- Running docking 3.7 - JJI currently working on this.
- Running DOCK 3.7 - this seems to be slightly dated.
- INDOCK 3.7 - file format used by DOCK 3.7
- Interpreting the OUTDOCK 3.7 file.
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
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.
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/.