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

Jaume Bonet
  • Structural Bioinformatics Group (GRIB), Department of Experimental and Life Sciences, University Pompeu Fabra, Barcelona, Catalonia, Spain
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Andras Fiser
  • Albert Einstein College of Medicine, Department of Systems and Computational Biology, Bronx, NY, USA
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Baldo Oliva
  • Structural Bioinformatics Group (GRIB), Department of Experimental and Life Sciences, University Pompeu Fabra, Barcelona, Catalonia, Spain
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Narcis Fernandez-Fuentes
  • Corresponding author
  • Structural Bioinformatics Group (GRIB), Department of Experimental and Life Sciences, University Pompeu Fabra, Barcelona, Catalonia, Spain
  • Email
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  • De Gruyter OnlineGoogle Scholar
Published Online: 2014-11-27 | DOI: https://doi.org/10.1515/bams-2014-0016

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.

Keywords: loop structure prediction; protein loops; protein secondary structures; protein structure design; protein structure prediction; protein supersecondary structures

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About the article

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:


Received: 2014-09-10

Accepted: 2014-10-15

Published Online: 2014-11-27

Published in Print: 2014-12-19


Citation Information: Bio-Algorithms and Med-Systems, ISSN (Online) 1896-530X, ISSN (Print) 1895-9091, DOI: https://doi.org/10.1515/bams-2014-0016.

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