DOCK 3.8: Difference between revisions
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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 specialized purpose. | |||
* dock3 : the fortran source code | |||
* pydock3 : the scripts and executables to run docking & parameter optimization | |||
* ligdock3 : the ligand building scripts used by ZINC-22. | |||
* SUBDOCK : scripts for submitting docking workloads to SLURM/SGE/Native | |||
* docktop : scripts for extracting top results from docking campaigns | |||
* zinc22-3d-submit : scripts for submitting ligand building workloads to SLURM/SGE | |||
* DOCK : legacy repository, still being used & updated (for now) | |||
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 install DOCK 3.8]] | ||
[[How to dock in DOCK3.8]] | [[SUBDOCK_DOCK3.8|How to dock in DOCK3.8]] | ||
[[Docking Analysis in DOCK3.8]] | [[Docking Analysis in DOCK3.8]] | ||
[[ | [[DOCK_3.8:How_to_install_pydock3|Installing pydock3]] | ||
[[Dockopt_(pydock3_script)|Running pydock3/dockopt (new blastermaster script- automatic optimization!)]] | |||
[[Blastermaster_(pydock3_script)|Running pydock3/blastermaster (classic blastermaster script - generate grid files)]] | |||
How to run DOCK/LSD in AWS, follow our tutorial, starting with setting up an AWS account. [[AWS:Set up account]] | |||
DOCK 3.8. | [[Building_The_3D_Pipeline_ZINC22| 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. | |||
[[How_to_compile_DOCK| How to compile DOCK 3.8]] | |||
== Availability == | == Availability == | ||
DOCK 3.8 is installed on our cluster and on Wynton. It is available on AWS | 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 == | == General Use == | ||
| Line 31: | Line 56: | ||
During development, this was the script we used to explain how to dock: | During development, this was the script we used to explain how to dock: | ||
[[How to dock in DOCK3.8]] | [[How to dock in DOCK3.8]] | ||
[[Category:DOCK 3.8]] | [[Category:DOCK 3.8]] | ||
Latest revision as of 17:06, 8 April 2023
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 specialized purpose.
* dock3 : the fortran source code * pydock3 : the scripts and executables to run docking & parameter optimization * ligdock3 : the ligand building scripts used by ZINC-22. * SUBDOCK : scripts for submitting docking workloads to SLURM/SGE/Native * docktop : scripts for extracting top results from docking campaigns * zinc22-3d-submit : scripts for submitting ligand building workloads to SLURM/SGE * DOCK : legacy repository, still being used & updated (for now)
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.
Running pydock3/dockopt (new blastermaster script- automatic optimization!)
Running pydock3/blastermaster (classic blastermaster script - generate grid files)
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