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

Jaume Bonet 1 , Andras Fiser 2 , Baldo Oliva 1  and Narcis Fernandez-Fuentes 1
  • 1 Structural Bioinformatics Group (GRIB), Department of Experimental and Life Sciences, University Pompeu Fabra, Barcelona, Catalonia, Spain
  • 2 Albert Einstein College of Medicine, Department of Systems and Computational Biology, Bronx, NY, USA
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.

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The journal Bio-Algorithms and Med-Systems provides a forum for the exchange of information in the interdisciplinary fields of computational methods applied in medicine presenting new algorithms and databases that allow the progress in collaboration between medicine, informatics, physics, and biochemistry.

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