Difference between revisions of "DOCK 3.8"

From DISI
Jump to navigation Jump to search
(asdf)
 
m (asdf)
 
(9 intermediate revisions by 2 users not shown)
Line 1: Line 1:
DOCK 3.8 is the new version (Jan 2021) of ZINC.  
+
DOCK 3.8 has been the primary version of DOCK 3 since January 2021.
DOCK 3.8.0 is the alpha version, currently in the dev branch. It became available for download in Jan 2021.  
+
 
 +
DOCK 3.8 is now organized in three separate github repos.
 +
* Dock3 - the fortran source code
 +
* PyDOCK3 - the scripts and executables to run docking
 +
* LigDOCK3 - the ligand building scripts used by ZINC-22.
 +
 
 +
DOCK 3.8 has been extensively reorganized from DOCK 3.7.
 +
 
 +
How to get DOCK 3.8. Use the DOCK license server dock.compbio.ucsf.edu. If you are a developer, fork the relevant repo.
 +
 
 +
[[How to install DOCK 3.8]]
 +
 
 +
[[How to dock in DOCK3.8]]
 +
 
 +
[[Docking Analysis in DOCK3.8]]
 +
 
 +
How to run DOCK/LSD in AWS, follow our tutorial, starting with setting up an AWS account. [[AWS:Set up account]]
 +
 
 +
[[ZINC-22:3D Building | how to build libraries for DOCK 3.8]]
 +
Please note that you only need to build libraries if you do not want to use ZINC-22, and if you do not want to use the free 3D molecule building service in TLDR.docking.org.
 +
 
 +
[[Programming DOCK 3.8]]
 +
DOCK 3.8.5 is the current production version of DOCK 3, as of Sept 1, 2022.
 +
If you wish to help develop DOCK 3.8, please write to us. 
 +
 
 +
== Availability ==
 +
DOCK 3.8 is installed on our cluster and on Wynton. It is available on AWS and OCI as a docker container. The software has never been easier to install (low bar!).  It should be runnable on any modern HPC platform. We recommend using an OS were python 3.8 or later is installed by default, however, you should be able to install python 3.8 or later on older equipment.
 +
 
 +
== General Use ==
 +
Mechanically, docking has the following steps.
 +
* prepare gridfiles (dockfiles)
 +
* select database subset to run
 +
* move all files to the target platform
 +
* run docking at scale
 +
* merge the results (top_poses.py)
 +
* move results back to your server.
 +
* process the results (interaction fingerprint, strain filter, clustering, manual review)
 +
* final re-extract of top poses for hit picking party.
 +
* archive the results.
 +
 
 +
== Step by Step instructions ==
 +
During development, this was the script we used to explain how to dock:
 +
[[How to dock in DOCK3.8]]
  
 
[[Category:DOCK 3.8]]
 
[[Category:DOCK 3.8]]

Latest revision as of 23:21, 14 September 2022

DOCK 3.8 has been the primary version of DOCK 3 since January 2021.

DOCK 3.8 is now organized in three separate github repos.

* Dock3 - the fortran source code 
* PyDOCK3 - the scripts and executables to run docking
* LigDOCK3 - the ligand building scripts used by ZINC-22. 

DOCK 3.8 has been extensively reorganized from DOCK 3.7.

How to get DOCK 3.8. Use the DOCK license server dock.compbio.ucsf.edu. If you are a developer, fork the relevant repo.

How to install DOCK 3.8

How to dock in DOCK3.8

Docking Analysis in DOCK3.8

How to run DOCK/LSD in AWS, follow our tutorial, starting with setting up an AWS account. AWS:Set up account

how to build libraries for DOCK 3.8 Please note that you only need to build libraries if you do not want to use ZINC-22, and if you do not want to use the free 3D molecule building service in TLDR.docking.org.

Programming DOCK 3.8 DOCK 3.8.5 is the current production version of DOCK 3, as of Sept 1, 2022. If you wish to help develop DOCK 3.8, please write to us.

Availability

DOCK 3.8 is installed on our cluster and on Wynton. It is available on AWS and OCI as a docker container. The software has never been easier to install (low bar!). It should be runnable on any modern HPC platform. We recommend using an OS were python 3.8 or later is installed by default, however, you should be able to install python 3.8 or later on older equipment.

General Use

Mechanically, docking has the following steps.

  • prepare gridfiles (dockfiles)
  • select database subset to run
  • move all files to the target platform
  • run docking at scale
  • merge the results (top_poses.py)
  • move results back to your server.
  • process the results (interaction fingerprint, strain filter, clustering, manual review)
  • final re-extract of top poses for hit picking party.
  • archive the results.

Step by Step instructions

During development, this was the script we used to explain how to dock: How to dock in DOCK3.8