pbxplore 1.4.0

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

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:

• 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:

$ 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.

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 https://doi.org/10.7717/peerj.4013 (2017).

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.