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PBxplore is a suite of tools dedicated to Protein Block (PB) analysis.
Protein Blocks are structural prototypes defined by
de Brevern et al <https://www.ncbi.nlm.nih.gov/pubmed/11025540>
_. 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).
.. image:: https://raw.githubusercontent.com/pierrepo/PBxplore/master/doc/source/img/PBs.jpg :alt: PBs
Figure 1. Schematic representation of the sixteen protein blocks,
labeled from a to p (Creative commons 4.0 CC-BY <https://creativecommons.org/licenses/by/4.0/>
_).
PBxplore provides both a Python library and command-line tools. Basically, PBxplore can:
PBxplore requires:
NumPy <http://numpy.scipy.org/>
, Matplotlib <http://matplotlib.org/>
, MDAnalysis <https://code.google.com/p/mdanalysis/>
_ (version >= 0.11).Optionally, PBxplore can use:
WebLogo 3 <http://weblogo.threeplusone.com/>
_ to create logo from PB sequences.Once dependencies installed, the most straightforward way is to use pip
:
.. code-block:: bash
$ pip install pbxplore
PBxplore can also be installed for the current user only:
.. code-block:: bash
$ pip install --user pbxplore
All documentation are hosted by Read The Docs and can be found here <https://pbxplore.readthedocs.org/en/latest/>
_.
If you use PBxplore, please cite this tool as:
Barnoud J, Santuz H, Craveur P, Joseph AP, Jallu V, de Brevern AG, Poulain P, | PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks | PeerJ 5:e4013 <https://doi.org/10.7717/peerj.4013> _ (2017). |
---|
The published version (1.3.8) is archived in Zenodo |zenodo-badge|
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PBxplore is a research software and has been developped by:
If you want to report a bug, request a feature,
use the GitHub issue system <https://github.com/pierrepo/PBxplore/issues>
_.
PBxplore is licensed under The MIT License <https://github.com/pierrepo/PBxplore/blob/master/LICENSE>
_.