pbxplore 1.1

# PBxplore [](https://travis-ci.org/pierrepo/PBxplore)

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PBxplore is a suite of tools dedicated to Protein Block analysis. Protein Blocks are structural prototypes defined by [de Brevern](http://www.dsimb.inserm.fr/~debrevern/index.php) et al [1]. 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](https://creativecommons.org/licenses/by/4.0/)).

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/](https://pbxplore.readthedocs.org/en/latest/).

## Download

• [Get latest zip archive](https://github.com/pierrepo/PBxplore/archive/master.zip)

• Clone repository: git clone git@github.com:pierrepo/PBxplore.git or git clone https://github.com/pierrepo/PBxplore.git

## Requirements

PBxplore requires:

• Python 2.7 or Python 3.x (>= 3.3)

• the [NumPy](http://numpy.scipy.org/ “NumPy”) Python library,

Optionally, PBxplore can use:

• the [MDAnalysis](https://code.google.com/p/mdanalysis/) Python library (version >= 0.11) to read MD trajectories generated by Gromacs (.xtc files),

• [Mapltolib](http://matplotlib.org/) to generate plots.

• [WebLogo 3](http://weblogo.threeplusone.com/) to create logo from PB sequences.

## Documentation

All documentation are hosted by Read The Docs and can be found [here](https://pbxplore.readthedocs.org/en/latest/).

## 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](https://github.com/pierrepo/PBxplore/issues>).

## Licence

PBxplore is licensed under [The MIT License](https://github.com/pierrepo/PBxplore/blob/master/LICENSE).

## References [1] A. G. de Brevern, C. Etchebest and S. Hazout. Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks. Proteins 41: 271-288 (2000).