https://github.com/pierrepo/pbxplore
A suite of tools to explore protein structures with Protein Blocks :snake:
https://github.com/pierrepo/pbxplore
bioinformatics-analysis protein python structure
Last synced: 3 months ago
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A suite of tools to explore protein structures with Protein Blocks :snake:
- Host: GitHub
- URL: https://github.com/pierrepo/pbxplore
- Owner: pierrepo
- License: mit
- Created: 2013-06-14T16:00:28.000Z (over 12 years ago)
- Default Branch: master
- Last Pushed: 2021-01-27T14:45:42.000Z (about 5 years ago)
- Last Synced: 2025-10-11T04:04:03.032Z (5 months ago)
- Topics: bioinformatics-analysis, protein, python, structure
- Language: Python
- Homepage: https://pbxplore.readthedocs.org/en/latest/
- Size: 50.9 MB
- Stars: 29
- Watchers: 7
- Forks: 15
- Open Issues: 6
-
Metadata Files:
- Readme: README.rst
- Changelog: CHANGELOG
- License: LICENSE
- Zenodo: .zenodo.json
Awesome Lists containing this project
README
PBxplore
========
.. image:: https://img.shields.io/badge/Python-3.6%203.8-brightgreen.svg
:alt: Python version
:target: https://pypi.python.org/pypi/pbxplore
.. image:: https://badge.fury.io/py/pbxplore.svg
:alt: PyPI PBxplore version
:target: https://pypi.python.org/pypi/pbxplore
.. image:: https://github.com/pierrepo/PBxplore/workflows/GitHub%20CI%20code/badge.svg
:alt: GitHub Actions build status
:target: https://github.com/pierrepo/PBxplore/actions?query=workflow%3A%22GitHub+CI+code%22
.. image:: https://github.com/pierrepo/PBxplore/workflows/GitHub%20CI%20doc/badge.svg
:alt: GitHub Actions build documentation status
:target: https://github.com/HubLot/PBxplore/actions?query=workflow%3A%22GitHub+CI+doc%22
.. image:: https://readthedocs.org/projects/pbxplore/badge/?version=latest
:alt: PBxplore documentation
:target: https://pbxplore.readthedocs.org/en/latest/
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.598132.svg
:alt: Zenodo badge
:target: https://doi.org/10.5281/zenodo.598132
**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).
.. 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 `_).
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 `_, `Matplotlib `_, `MDAnalysis `_ (version >= 0.11).
Optionally, PBxplore can use:
* `WebLogo 3 `_ 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 `_.
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 ``_ (2017).
|
The published version (1.3.8) is archived in Zenodo |zenodo-badge|
.. |zenodo-badge| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1016257.svg
:alt: Zenodo badge
:target: https://doi.org/10.5281/zenodo.1016257
and Software Heritage |SWH-badge|
.. |SWH-badge| image:: https://archive.softwareheritage.org/badge/swh:1:dir:4260527877ab457f65eb1299437cf022301a4788/
:alt: Software Heritage badge
:target: https://archive.softwareheritage.org/swh:1:dir:4260527877ab457f65eb1299437cf022301a4788;origin=https://github.com/pierrepo/PBxplore;visit=swh:1:snp:fb4066f408260c44decc7cac3624b56747a3de69;anchor=swh:1:rev:ba1290912cd65c86a01f70716e1d3133778bba75/
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 `_.
License
-------
PBxplore is licensed under `The MIT License `_.