PBxplore

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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).

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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:

• assign PBs from a single PDB, many PDBs or a molecular dynamics simulation trajectory.
• use analysis tools to perform statistical analysis on PBs.
• use analysis tools to study protein flexibility and deformability.

Requirements

PBxplore requires:

• Python 3.x (>= 3.6)
• Python modules: 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.

Installation

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

Documentation

All documentation are hosted by Read The Docs and can be found here <https://pbxplore.readthedocs.org/en/latest/>_.

Citation

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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Contact & Support

PBxplore is a research software and has been developped by:

• Pierre Poulain, "Mitochondria, Metals and Oxidative Stress" group, Institut Jacques Monod, UMR 7592, Univ. Paris, CNRS, France.
• Jonathan Barnoud, University of Groningen, Groningen, The Netherlands.
• Hubert Santuz, Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique, Paris, France.
• Alexandre G. de Brevern & Gabriel Cretin, DSIMB, INSERM, UMR_S 1134, INTS, Univ Paris, Paris, France.

If you want to report a bug, request a feature, use the GitHub issue system <https://github.com/pierrepo/PBxplore/issues>_.

License

PBxplore is licensed under The MIT License <https://github.com/pierrepo/PBxplore/blob/master/LICENSE>_.