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Project Description

PBxplore is a suite of tools dedicated to Protein Block (PB) analysis. Protein Blocks are structural prototypes defined by de Brevern et al. The 3-dimensional local structure of a protein backbone can be modelized as an 1-dimensional sequence of PBs. In principle, any conformation of any amino acid could be represented by one of the sixteen available Protein Blocks (see Figure 1).

Figure 1. Schematic representation of the sixteen protein blocks, labeled from a to p (Creative commons 4.0 CC-BY).

PBxplore provides both a Python library and command-line tools. Basically, PBxplore can:

  • assign PBs from either a PDB or either a molecular dynamics trajectory.
  • use analysis tools to perform statistical analysis on PBs.
  • use analysis tools to study protein flexibility and deformability.

For details, see the documentation at https://pbxplore.readthedocs.org/en/latest/.

Requirements

PBxplore requires:

  • Python 2.7 or Python 3.x (>= 3.3)
  • the NumPy Python library,

Optionally, PBxplore can use:

  • the MDAnalysis Python library (version >= 0.11) to read MD trajectories generated by Gromacs (.xtc files),
  • the Matplotlib Python library to generate plots.
  • WebLogo 3 to create logo from PB sequences.

Installation

Once dependencies installed, the most straightforward way is to use pip:

$ pip install pbxplore

PBxplore can also be installed for the current user only:

$ pip install --user pbxplore

Documentation

All documentation are hosted by Read The Docs and can be found here.

Contact & Support

PBxplore is a research software and has been developped by:

  • Pierre Poulain, DSIMB, Ets Poulain, Pointe-Noire, Congo
  • Jonathan Barnoud, University of Groningen, Groningen, The Netherlands
  • Hubert Santuz, DSIMB, Paris, France
  • Alexandre G. de Brevern, DSIMB, Paris, France

If you want to report a bug, request a feature, use the GitHub issue system.

License

PBxplore is licensed under The MIT License.

Release History

Release History

1.3.1

This version

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TODO: Figure out how to actually get changelog content.

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1.3

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1.2

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TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

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1.1

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
pbxplore-1.3.1.tar.gz (17.4 MB) Copy SHA256 Checksum SHA256 Source May 19, 2016

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