PBxplore is a suite of tools dedicated to Protein Block analysis.
Project description
# PBxplore [![Build Status](https://travis-ci.org/pierrepo/PBxplore.svg?branch=master)](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).
![PBs](doc/source/img/PBs.jpg “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:
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).
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