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pbxplore

A suite of tools to explore protein structures with Protein Blocks :snake:

https://github.com/pierrepo/pbxplore

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 8 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov, zenodo.org
  • ✓
    Committers with academic emails
    1 of 7 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.6%) to scientific vocabulary

Keywords

bioinformatics-analysis protein python structure
Last synced: 6 months ago · JSON representation

Repository

A suite of tools to explore protein structures with Protein Blocks :snake:

Basic Info
Statistics
  • Stars: 29
  • Watchers: 7
  • Forks: 15
  • Open Issues: 6
  • Releases: 5
Topics
bioinformatics-analysis protein python structure
Created over 12 years ago · Last pushed about 5 years ago
Metadata Files
Readme Changelog License Zenodo

README.rst 

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 `_.

Owner

  • Name: Pierre Poulain
  • Login: pierrepo
  • Kind: user
  • Location: Paris, France

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 540
  • Total Committers: 7
  • Avg Commits per committer: 77.143
  • Development Distribution Score (DDS): 0.481
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Pierre Poulain p****n@c****t 280
Jonathan Barnoud j****n@b****t 133
Hubert h****z@g****m 107
gabrielctn g****n@g****m 11
Pierrick p****r@i****r 5
Pierre Poulain b****i@c****) 3
Alexandre G. de Brevern a****7 1
Committer Domains (Top 20 + Academic)
citron.(none): 1 inserm.fr: 1 barnoud.net: 1 cupnet.net: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 44
  • Total pull requests: 56
  • Average time to close issues: 4 months
  • Average time to close pull requests: 6 days
  • Total issue authors: 6
  • Total pull request authors: 4
  • Average comments per issue: 3.91
  • Average comments per pull request: 3.21
  • Merged pull requests: 53
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • pierrepo (15)
  • jbarnoud (14)
  • HubLot (8)
  • alexdb27 (5)
  • TJRnarwani (1)
  • jmaupetit (1)
Pull Request Authors
  • HubLot (29)
  • pierrepo (16)
  • jbarnoud (9)
  • gabrielctn (2)
Top Labels
Issue Labels
documentation (9) install (5) clustering (3) enhancement (3) bug (2) wontfix (2) Critical (1) duplicate (1)
Pull Request Labels
install (1) enhancement (1) clustering (1) documentation (1)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 24 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 2
  • Total versions: 12
  • Total maintainers: 1
pypi.org: pbxplore

PBxplore is a suite of tools dedicated to Protein Block analysis.

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 24 Last month
Rankings
Forks count: 8.9%
Dependent packages count: 10.0%
Dependent repos count: 11.6%
Stargazers count: 12.0%
Average: 17.1%
Downloads: 42.9%
Maintainers (1)
pierrepo
Last synced: 6 months ago

Dependencies

dev_requirements.txt pypi
  • coverage * development
  • pytest * development
  • sphinx >=1.3.1 development
  • sphinxcontrib-napoleon * development
doc_requirements.txt pypi
  • biopython *
  • ipython *
  • jupyter *
  • matplotlib *
  • nbconvert *
  • nbsphinx *
  • numpy *
  • sphinx >=1.3.1
  • sphinx_rtd_theme *
  • sphinxcontrib-napoleon *
  • weblogo *
setup.py pypi
  • MDAnalysis >=0.11
  • matplotlib *
  • numpy *