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 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/.
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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 Python library,
Optionally, PBxplore can use:
the MDAnalysis Python library (version >= 0.11) to read MD trajectories generated by Gromacs (.xtc files),
the Matplotlib Python library to generate plots.
WebLogo 3 to create logo from PB sequences.
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.
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