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• How to install DOCK 3.8
  ...red to as DOCKEXEC, or simply DOCK. This page describes how to gain access to this program. Please obtain a license via the DOCK license server [[https://dock.docking.org/Online_Licensing/dock_license_application.html]] and download t
  2 KB (274 words) - 04:52, 3 March 2023
• DOCK 3.8:How to install pydock3
  ...hon package wrapping the [[DOCK|DOCK Fortran program]] that provides tools to help standardize and automate the computational methods employed in molecul Note: if you are at UCSF on gimel or wynton, you do not need to install, the software is already locally maintained.
  923 bytes (140 words) - 23:37, 2 November 2022
• DOCK 3.8:How to build a release
  ...rmal definition of a release of the [https://dock.compbio.ucsf.edu/ ''UCSF DOCK''] software suite * (e.g., build pip-installable wheel file using [[Python Poetry|poetry]]).
  3 KB (491 words) - 21:46, 22 February 2024

Page text matches

• How to install pydock3
  #REDIRECT [[DOCK 3.8:How to install pydock3]]
  45 bytes (6 words) - 19:46, 12 September 2022
• How to install DOCK 3.8
  ...red to as DOCKEXEC, or simply DOCK. This page describes how to gain access to this program. Please obtain a license via the DOCK license server [[https://dock.docking.org/Online_Licensing/dock_license_application.html]] and download t
  2 KB (274 words) - 04:52, 3 March 2023
• DOCK 3.8
  DOCK 3.8 has been the primary version of DOCK 3 since January 2021. DOCK 3.8 is now organized into a number of smaller repositories, each with a special
  3 KB (413 words) - 17:06, 8 April 2023
• DOCK3.8:Pydock3
  ...Blaster, originally published in 2009, and blastermaster.py, part of the [[DOCK 3.7]] release in 2012. ...docking configurations, perform retrospective docking on them in parallel using a specified job scheduler (e.g. Slurm), and analyze the results.
  2 KB (225 words) - 01:51, 24 August 2023
• DOCK 3.7
  ...grams developed and used by the [[Shoichet Lab]]. Please read and cite the DOCK 3.7 paper ...] with many improved features. DOCK 3.7 comes with all the tools necessary to prepare a
  6 KB (844 words) - 17:03, 27 July 2021
• Zinc22 restart wynton
  This is a temporary page describing how to use DOCK 3.8 restartable on Wynton. * rename your dockfiles to dockfiles.${indockhash} where
  985 bytes (161 words) - 05:46, 19 January 2021
• How to create actives and decoys for dockopt
  How to create actives and decoys for dockopt Create decoys using TLDR. or command line
  383 bytes (63 words) - 21:53, 16 February 2023
• AWS:Cleanup
  ...8-10 weeks when you have purchased compounds and tested them and you want to do some follow up docking. ...of every molecule, so you might have to re-dock some tranches if you want to look at that.
  1 KB (215 words) - 21:29, 14 September 2022
• Welcome web user
  ...], and is a work in progress. [https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing] ...re || Latest are [[DOCK 3.8]] and [[DOCK 6.11]] [https://dock.docking.org dock.docking.org]
  4 KB (488 words) - 20:55, 26 April 2024
• Main Page
  ...], and is a work in progress. [https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing] ...re || Latest are [[DOCK 3.8]] and [[DOCK 6.11]] [https://dock.docking.org dock.docking.org]
  4 KB (488 words) - 20:56, 26 April 2024
• ZINC22:Singularity
  Info on using ZINC-22 3D building in singularity. == how to use the singularity image ==
  2 KB (355 words) - 21:40, 9 February 2021
• DOCK38:Job configuration
  ...l for a job configuration file that can be used to manage LSD jobs in DOCK 3.8 ** lsd controls *how* the job runs on that platform. particularly *which* molecules.
  1 KB (194 words) - 19:01, 1 September 2022
• AWS:Upload files for docking
  * You've followed the tutorial for setting up the environment: [[AWS DOCK Environment Setup]] ...ave the aws-setup docker image installed on your machine (we will continue using it in this tutorial)
  5 KB (797 words) - 22:10, 11 October 2022
• SUBDOCK DOCK3.8
  ...fectly capable of running DOCK 3.7 workloads, though some features of DOCK 3.8 will not be taken advantage of. '''IMPORTANT: subdock.bash expects to live in the same directory as rundock.bash!!!'''
  12 KB (1,896 words) - 02:59, 28 December 2023
• Docking Analysis in DOCK3.8
  = Python 3.8+ = The simplest way to source python 3.8+ is to just install via conda.
  5 KB (837 words) - 04:34, 3 March 2023
• DOCK:History
  The History of [[DOCK]], longish version ...es of an individual molecule, or be used to screen a database of molecules to identify potential ligands.
  11 KB (1,545 words) - 17:01, 27 January 2021
• AWS:Merge and download results
  github personal access token & DOCK github repository access rights (https://docs.github.com/en/authentication/ ...pulling the DOCK repository. You can email us at bkslab for access to the DOCK repository.
  6 KB (897 words) - 21:30, 14 September 2022
• How to dock in DOCK3.8
  How to dock in DOCK 3.8.0 Related page: Docking Analysis with DOCK 3.8
  16 KB (2,599 words) - 22:28, 1 December 2022
• GPU DOCK
  ...that utilizes GPU acceleration via CUDA. Currently (as of April 2023) GPU DOCK uses the GPU for parallel scoring and only supports Van der Waals, electros =Running and Building GPU DOCK=
  20 KB (3,437 words) - 20:50, 22 April 2023
• AWS:Submit docking job
  ...older, it will be used during submission. INDOCK configuration is expected to be located within the dockfiles folder. ...to dockable db2.tgz files accessible by the environment you are submitting to. For example, here is a short but valid input list:
  8 KB (1,398 words) - 22:11, 11 October 2022