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

PeerJ

Hubert Santuz¹  Agnel Praveen Joseph¹  Pierrick Craveur¹  Jonathan Barnoud¹  Pierre Poulain¹  Alexandre G. de Brevern¹  Vincent Jallu² 

[1] INSERM, U 1134, DSIMB, Paris, France;Platelet Unit, INTS, Paris, France;

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

DOI  :  10.7717/peerj.4013

来源: DOAJ

【 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】

Unknown