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

PeerJ

article

Jonathan Barnoud¹  Hubert Santuz¹  Pierrick Craveur¹  Agnel Praveen Joseph¹  Vincent Jallu⁹  Alexandre G. de Brevern¹  Pierre Poulain¹ 

[1] INSERM;Univ. Paris Diderot;Institut National de la Transfusion Sanguine;Laboratoire d’Excellence GR-Ex;Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen;Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique;Department of Integrative Structural and Computational Biology, The Scripps Research Institute;Birkbeck College, University of London;Platelet Unit;Mitochondria, Metals and Oxidative Stress Group, Institut Jacques Monod

关键词: Protein blocks;    Deformability;    Python;    Protein;    Structure;    Structural alphabet;   

DOI  :  10.7717/peerj.4013

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY