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Springer (part of Springer Nature), Biophysical Reviews, 3(2), p. 137-145

DOI: 10.1007/s12551-010-0036-1

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A short survey on protein blocks

Journal article published in 2010 by Agnel Praveen Joseph, Garima Agarwal, Swapnil Mahajan ORCID, Jean-Christophe Gelly, Lakshmipuram S. Swapna, Bernard Offmann, Frédéric Cadet, Aurélie Bornot, Manoj Tyagi, Hélène Valadié, Bohdan Schneider ORCID, Catherine Etchebest, Narayanaswamy Srinivasan, Alexandre G. de Brevern
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This paper is available in a repository.

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Abstract

Protein structures are classically described in terms of secondary structures. Even if the regular secondary structures have relevant physical meaning, their recognition from atomic coordinates has some important limitations such as uncertainties in the assignment of boundaries of helical and β-strand regions. Further, on an average about 50% of all residues are assigned to an irregular state, i.e., the coil. Thus different research teams have focused on abstracting conformation of protein backbone in the localized short stretches. Using different geometric measures, local stretches in protein structures are clustered in a chosen number of states. A prototype representative of the local structures in each cluster is generally defined. These libraries of local structures prototypes are named as "structural alphabets". We have developed a structural alphabet, named Protein Blocks, not only to approximate the protein structure, but also to predict them from sequence. Since its development, we and other teams have explored numerous new research fields using this structural alphabet. We review here some of the most interesting applications.