Welcome to PBxplore’s documentation!

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

Protein Blocks (PBs) are structural prototypes defined by de Brevern et al [1]. 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.

_images/PBs.jpg

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 (Utilization). For some features (reading trajectory, plots), PBxplore requires some optional dependencies (Installation). Basically, PBxplore can:

  • assign PBs from either a PDB or either a molecular dynamics trajectory (PB assignation).
  • use analysis tools to perform statistical analysis on PBs (Statistics).
  • use analysis tools to study protein flexibility and deformability (Analyzis).

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

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 Diderot, CNRS, Sorbonne Paris Cité, 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, DSIMB, INSERM, U 1134, INTS, Paris, France.

If you want to report a bug or request a feature, please use the GitHub issue system.

Licence

PBxplore is licensed under The MIT License.

[1]
    1. de Brevern, C. Etchebest, and S. Hazout. Bayesian Probabilistic Approach for Predicting Backbone Structures in Terms of Protein Blocks. Proteins 41:271-87 (2000).