BIROn - Birkbeck Institutional Research Online

    PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks

    Barnoud, J. and Santuz, H. and Craveur, P. and Joseph, Agnel Praveen and Jallu, V. and de Brevern, A.G. and Poulain, P. (2017) PBxplore: a tool to analyze local protein structure and deformability with Protein Blocks. PeerJ 5 , e4013. ISSN 2167-8359.

    [img]
    Preview
    Text
    20563.pdf - Published Version of Record
    Available under License Creative Commons Attribution.

    Download (5MB) | Preview

    Abstract

    This paper describes the development and application of a suite of tools, called PBxplore, to analyze the dynamics and deformability of protein structures using Protein Blocks (PBs). Proteins are highly dynamic macromolecules, and a classical way to analyze their inherent flexibility is to perform molecular dynamics simulations. The advantage of using small structural prototypes such as PBs is to give a good approximation of the local structure of the protein backbone. More importantly, by reducing the conformational complexity of protein structures, PBs allow analysis of local protein deformability which cannot be done with other methods and had been used efficiently in different applications. PBxplore is able to process large amounts of data such as those produced by molecular dynamics simulations. It produces frequencies, entropy and information logo outputs as text and graphics. PBxplore is available at https://github.com/pierrepo/PBxplore and is released under the open-source MIT license.

    Metadata

    Item Type: Article
    School: Birkbeck Faculties and Schools > Faculty of Science > School of Natural Sciences
    Depositing User: Administrator
    Date Deposited: 08 Dec 2017 14:25
    Last Modified: 02 Aug 2023 17:37
    URI: https://eprints.bbk.ac.uk/id/eprint/20563

    Statistics

    Activity Overview
    6 month trend
    268Downloads
    6 month trend
    179Hits

    Additional statistics are available via IRStats2.

    Archive Staff Only (login required)

    Edit/View Item Edit/View Item