DOCK 3.7: Difference between revisions
(asdf) |
(asdf) |
||
| Line 1: | Line 1: | ||
= About = | = About = | ||
DOCK 3.7 | |||
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 | 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/ http://dock.compbio.ucsf.edu/DOCK3.7/]. | |||
{{TOCright}} | {{TOCright}} | ||
= Start here = | = Start here = | ||
* [[So you want to set up a lab]] | * [[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]] | ||
| Line 43: | Line 45: | ||
= Available Libraries = | = Available Libraries = | ||
* [[ZINC Subset DB2 file locations]] | * [[ZINC Subset DB2 file locations]] | ||
* how to get db2 files from zinc15.docking.org | |||
= Previous verisons = | = Previous verisons and compatibility = | ||
DOCK 3.7 is part of the [[DOCK 3]] series. | 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/]. | ||
= | = Implementation = | ||
DOCK 3.7 is written in Fortran and some C. Scripts are mostly in [[python]] and perl. | 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 06:35, 3 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
- So you want to set up a lab - only if you don't already have hardware ready.
- Install DOCK 3.7
- DOCK 3.7 2014/09/25 FXa Tutorial
- DOCK 3.7 2015/04/15 abl1 Tutorial
- Getting started with DOCK 3.7
- Blastermaster - Prepare input for and then run DOCK 3.7.
- Ligand preparation 3.7 - Create dockable databases for DOCK 3.7.
- Ligand preparation - different version.
- Mol2db2 Format 2 - details on the database formate.
- Running docking 3.7 - how to actually run docking.
- DOCK 3.7 Development - for software developers
Prepare Receptor
Prepare Screening Library
- mol2db2 is the program that creates mol2db2 format database files which are read by DOCK 3.7
- ligand preparation 3.7
Running 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
- Analyzing DOCK Results
- Auto-DUD-E Test Set (external site)
Available Libraries
- ZINC Subset DB2 file locations
- how to get db2 files from zinc15.docking.org
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/.