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Licensed Unlicensed Requires Authentication Published by De Gruyter November 27, 2014

Smotifs as structural local descriptors of supersecondary elements: classification, completeness and applications

Jaume Bonet, Andras Fiser, Baldo Oliva and Narcis Fernandez-Fuentes

Abstract

Protein structures are made up of periodic and aperiodic structural elements (i.e., α-helices, β-strands and loops). Despite the apparent lack of regular structure, loops have specific conformations and play a central role in the folding, dynamics, and function of proteins. In this article, we reviewed our previous works in the study of protein loops as local supersecondary structural motifs or Smotifs. We reexamined our works about the structural classification of loops (ArchDB) and its application to loop structure prediction (ArchPRED), including the assessment of the limits of knowledge-based loop structure prediction methods. We finalized this article by focusing on the modular nature of proteins and how the concept of Smotifs provides a convenient and practical approach to decompose proteins into strings of concatenated Smotifs and how can this be used in computational protein design and protein structure prediction.


Corresponding author: Narcis Fernandez-Fuentes, Structural Bioinformatics Group (GRIB), Department of Experimental and Life Sciences, University Pompeu Fabra, C. Doctor Aiguader, 88, Barcelona 08003, Catalonia, Spain, E-mail:

Acknowledgments

This article is partially based on our previous publications [ref. 30–39, 41]. NFF acknowledges support from ACCIO, Generalitat of Catalunya under the TecnioSpring Program, project number TECSPR13-1-0008, REA grant agreement 600388. This work was supported by NIH grants GM094665 and GM096041 to AF. JB and BO acknowledge support from the Spanish Ministry of Economy under grant BIO2011-22568.

Author contributions: All authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.

Research funding: None declared.

Employment or leadership: None declared.

Honorarium: None declared.

Competing interests: The funding organization(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication.

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Received: 2014-9-10
Accepted: 2014-10-15
Published Online: 2014-11-27
Published in Print: 2014-12-19

©2014 by De Gruyter