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

Project Description

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).

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:

Optionally, PBxplore can use:

  • WebLogo 3 to create logo from PB sequences.

Installation

Once dependencies installed, the most straightforward way is to use pip:

$ pip install pbxplore

PBxplore can also be installed for the current user only:

$ pip install --user pbxplore

Documentation

All documentation are hosted by Read The Docs and can be found here.

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.

License

PBxplore is licensed under The MIT License.

Release History

Release History

This version
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1.3.7

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1.3.6

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1.3.5

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1.3.4

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1.3.3

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1.3.2

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1.3.1

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1.3

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1.2

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1.1

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
pbxplore-1.3.7.tar.gz (4.2 MB) Copy SHA256 Checksum SHA256 Source Aug 14, 2017

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