ProBiS H2O Plugin
We developed the ProBiS H2O approach, which enables identification of conserved water sites in proteins using experimental protein structures from the PDB or a set of custom protein structures available to the user. With a protein structure, a binding site or an individual water molecule as query.
ProBiS H2O Plugin
- ProBiS H2O plugin for PyMOL: ProBiS_H2O.py (download this file and install from local file in PyMOL's Plugin Manager)
- Whole package (see Manual Installation): probis-h2o-plugin.zip
ProBiS H2O Plugin User Guide / Tutorial
- ProBiS H2O plugin User Guide (this tutorial is a bit outdated): ProBiS_H2O_tutorial-user_guide_0_9.pdf
- Use 'Help' tag within the plugin to get the latest instructions
Versions and Release Notes
1.1.4 (Oct/18/2022)
- Fixed RCSB has changed the syntax required to access the cluster database
1.1.3 (Feb/01/2022)
- Fixed reading of PDB files
1.1.2 (Dec/10/2021)
- Improved Help tab
- Fixed some quirks on certain versions of PyMol
1.1.1 (Jun/11/2021)
- The plugin has been completely rewritten in Python 3 using Qt5 GUI
- Works with PyMol 2.3 and above
- Works on Linux (tested on Ubuntu 20.04) and Windows (tested on Windows 10)
- One of the new features is automatic updater
1.0.0
- This version works with older PyMols (versions 1.x), it is still available here: ProBiS_H2O_plugin.py
Installation
Download the ProBiS H2O plugin file and follow the instructions in User Guide / Tutorial file. This tutorial is a bit outdated, but may still contain some useful information. Importantly, the plugin should now automatically install its dependencies (scikit-learn). If this wouldn't work for some reason, look for suggestions in the tutorial. Also, the file that you download is just 'installer' script, which downloads the rest of the plugin from this page. This allows you to get the latest update of the plugin without manually reinstalling it - hopefully saving you some time.Manual Installation (optional)
If automatic installation fails for any reason (for instance our server might be unavailable), manual installation can be accomplished like this:
- Download probis-h2o-plugin.zip file, which contains the entire package.
- Extract it and find within the ".probisH2O" directory (the dot in front of the name means it is a hidden directory).
- Copy .probisH2O directory to your home directory.
- In the top directory of the extracted archive locate ProBiS_H2O.py and install it using Plugin Manager in PyMOL.
On the First Start
- Start the plugin: you can leave the version directory as is.
- If dependency (scikit-learn) is not already installed it should be installed automatically by the plugin. If this fails for some reason, you can manually install it with eg., 'pip3 install scikit-learn'
- Setup the database to unlock the plugin.
System Requirements
The ProBiS plugin has been developed for Linux and Windows environments with PyMOL version >= 2.3.Important Notes
- Before experimentation, database files need to be set-up, a process that can take a bit longer. Subsequent usage shoud be lightning-fast.
- Sometimes the "fetch/reset" button downloads the system at PyMol defaut visualisation settings. This is a PyMol inconsistency that can be resolved by simply fetching the system again.
Related Publications
Marko Jukič, Janez Konc, Stanislav Gobec, Dušanka Janežič. Identification of Conserved Water Sites in Protein Structures for Drug Design. J. Chem. Inf. Model., 2017, doi: 10.1021/acs.jcim.7b00443
Jukič, Marko, Janez Konc, Stanislav Gobec, Dušanka Janežič. Identification of Conserved Water Sites in Protein Structures for Drug Design. J. Chem. Inf. Model., 2017, doi: 10.1021/acs.jcim.7b00443
Jukic, M., Ilas, J., Brvar, M., Kikelj, D., Cesar, J., Anderluh, M. (2016) Linker-switch approach towards new ATP binding site inhibitors of DNA gyrase B. European Journal of Medicinal Chemistry, 125, 500-514.
Jukic, Marko, et al. Linker-switch approach towards new ATP binding site inhibitors of DNA gyrase B. European Journal of Medicinal Chemistry, 2017, 125, 500-514.
@article{jukic2017linker,
title={Linker-switch approach towards new ATP binding site inhibitors of DNA gyrase B},
author={Jukic, Marko, Marko Jukic, Jukic and Anderluh},
journal={European Journal of Medicinal Chemistry},
volume={125},
number={125},
year={2017},
publisher={Elsevier}
}
title={Linker-switch approach towards new ATP binding site inhibitors of DNA gyrase B},
author={Jukic, Marko, Marko Jukic, Jukic and Anderluh},
journal={European Journal of Medicinal Chemistry},
volume={125},
number={125},
year={2017},
publisher={Elsevier}
}
%0 Journal Article
%T Linker-switch approach towards new ATP binding site inhibitors of DNA gyrase B
%A Jukic, Marko
%A Ilas, Janez
%A Brvar, Matjaz
%A Kikelj, Danijel
%A Cesar, Jozko
%A Anderluh, Marko
%J European Journal of Medicinal Chemistry
%V 125
%N 125
%D 2017
%I Elsevier
%T Linker-switch approach towards new ATP binding site inhibitors of DNA gyrase B
%A Jukic, Marko
%A Ilas, Janez
%A Brvar, Matjaz
%A Kikelj, Danijel
%A Cesar, Jozko
%A Anderluh, Marko
%J European Journal of Medicinal Chemistry
%V 125
%N 125
%D 2017
%I Elsevier