DOCK Blaster: Difference between revisions

From DISI
Jump to navigation Jump to search
No edit summary
m (asdf)
 
(53 intermediate revisions by 3 users not shown)
Line 1: Line 1:
DOCK Blaster is a free web based molecular docking and virtual screening service, on the web at [http://blaster.docking.org].
DOCK Blaster is a program that does automatic docking.  


To get started, you will need the structure of the target in PDB format, and some specification of the binding site. Currently, we support one of two forms: * a) a docked ligand, which is used both as a control and indication of where to dock, in mol2 format. If you don't have a docked ligand, don't worry, you can also specify:
The first version of DOCK Blaster appeared in 2009. Please see [https://wiki.docking.org/index.php/Category:DOCK_Blaster Category:DOCK_Blaster]
* b) residues making up the binding site, in PDB format. The center of interia of these atoms should be about the same place that the center of a docked molecule would be.


That's really all you need to have to get started. If you don't have a particular project in mind, you may use some [[DOCK Blaster::Sample_Data Sample Data]] to experiment with. To read more, please consult the topics below.
A re-write of the idea of DOCK Blaster, blastermaster.py, was part of the [[DOCK 3.7]] release in 2012.  


== Before you get started ==
In 2022 there were major developments.  First, we reorganized the DOCK repo into three repos:
* [[DOCK Blaster:Preliminaries]]
* dock3 - the fortran source code and not much else
* pydock3 - all the scripts to run docking except for 3d ligand building
* ligdock3 - 3d ligand building pipeline


There is also
* cheminftools - various tools.


== Preparation and Docking ==
DOCK is distributed via the dock license server dock.compbio.ucsf.edu where it is licensed for free to academics and for a small fee to companies.
* [[DOCK Blaster:Prepare Input]]
** [[DOCK Blaster:Prepare Receptor]]
** [[DOCK Blaster:Prepare Ligand]]
** [[DOCK Blaster:Other Input Options]]
** [[DOCK Blaster:Input Troubleshooting]]
**  [[DOCK Blaster:Job Management]]


== Understanding the Results ==
The name of all the software together is "UCSF DOCK" and the current version is 3.8.1.0.0, so "UCSF DOCK 3.8.1.0.0"
* [[DOCK Blaster:Results]]
** [[DOCK Blaster:Initial Evaluation]]
** [[DOCK Blaster:Results Browser]]
** [[DOCK Blaster:Large Database Docking]]
** [[DOCK Blaster:Custom Database]]
** [[DOCK Blaster:Test Compounds]]


== Other information ==
The automatic pipeline to run docking is "dockopt", which is part of [[DOCK3.8:Pydock3 | pydock3]]
* [[DOCK Blaster:Philosophy]]
* [[DOCK Blaster:Annotations]]
* [[DOCK Blaster:History]]
* [[DOCK Blaster:Credits]]


How to cite DOCK Blaster. Please cite Huang, Shoichet, Irwin, "Benchmarking Sets for Molecular Docking", J Med Chem 2006, in press.
The website that allows free public preparation of receptors for docking is called "dockopt".  


We welcome your feedback about DOCK Blaster. Please write to us at comments at docking.org.
[[Category:DOCK 3.8]]

Latest revision as of 22:07, 16 September 2022

DOCK Blaster is a program that does automatic docking.

The first version of DOCK Blaster appeared in 2009. Please see Category:DOCK_Blaster

A re-write of the idea of DOCK Blaster, blastermaster.py, was part of the DOCK 3.7 release in 2012.

In 2022 there were major developments. First, we reorganized the DOCK repo into three repos:

  • dock3 - the fortran source code and not much else
  • pydock3 - all the scripts to run docking except for 3d ligand building
  • ligdock3 - 3d ligand building pipeline

There is also

  • cheminftools - various tools.

DOCK is distributed via the dock license server dock.compbio.ucsf.edu where it is licensed for free to academics and for a small fee to companies.

The name of all the software together is "UCSF DOCK" and the current version is 3.8.1.0.0, so "UCSF DOCK 3.8.1.0.0"

The automatic pipeline to run docking is "dockopt", which is part of pydock3

The website that allows free public preparation of receptors for docking is called "dockopt".

Retrieved from "http://wiki.docking.org/index.php?title=DOCK_Blaster&oldid=14819"