bio-pyvol 1.2.33

a PyMOL plugin and python package for visualization, comparison, and volume calculation of protein drug-binding sites

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title: 'PyVOL: Protein Pocket Visualization, Segmentation, and Characterization'

Overview

PyVOL is a python library packaged into a PyMOL GUI for identifying protein binding pockets, partitioning them into sub-pockets, and calculating their volumes. PyVOL can be run as a PyMOL plugin through its GUI or the PyMOL prompt, as an imported python library, or as a command-line program. Visualization of results is exclusively supported through PyMOL though exported surfaces are compatible with standard 3D geometry visualization programs.

Quick Installation into PyMOL

PyVOL can be installed into any python environment, but installing directly into PyMOL 2.0+ is easiest. Download the installer zip file and then use the plugin manager to install that file.

https://github.com/schlessingerlab/pyvol/blob/master/installers/pyvol-installer.zip

This installs the PyVOL GUI. Select PyVOL under the plugins menu, and then select Install from PyPI under the settings tab to fetch PyVOL and any missing dependencies. For academic users and non-academic users with the Schrodinger incentive PyMOL distribution, installation is now complete. For all others, see manual installation of msms.

Example Basic Run

The simplest calculation just using the PyMOL prompt is to load a protein of interest and then run the pocket command. This is an example for the Sorafenib-bound structure of BRAF:

fetch 1UWH
pocket "1UWH and chain B"

More Examples & Documentation

For more details on how to run PyVOL, example calculations, details on installation, and extensive documentation, look at the project documentation website:

https://schlessingerlab.github.com/pyvol