@article{Craveur2015, abstract = {Protein structures are valuable tools to understand protein function. Nonetheless, proteins are often considered as rigid macromolecules while their structures exhibit specific flexibility, which is essential to complete their functions. Analyses of protein structures and dynamics are often performed with a simplified three-state description, i.e., the classical secondary structures. More precise and complete description of protein backbone conformation can be obtained using libraries of small protein fragments that are able to approximate every part of protein structures. These libraries, called structural alphabets (SAs), have been widely used in structure analysis field, from definition of ligand binding sites to superimposition of protein structures. SAs are also well suited to analyze the dynamics of protein structures. Here, we review innovative approaches that investigate protein flexibility based on SAs description. Coupled to various sources of experimental data (e.g., B-factor) and computational methodology (e.g., Molecular Dynamic simulation), SAs turn out to be powerful tools to analyze protein dynamics, e.g., to examine allosteric mechanisms in large set of structures in complexes, to identify order/disorder transition. SAs were also shown to be quite efficient to predict protein flexibility from amino-acid sequence. Finally, in this review, we exemplify the interest of SAs for studying flexibility with different cases of proteins implicated in pathologies and diseases.}, author = {Craveur, Pierrick and Joseph, Agnel Praveen and Esque, Jeremy and Narwani, Tarun JaiRaj and Noël, Floriane and Shinada, Nicolas and Noël, Floriane and Goguet, Matthieu and Leonard, Sylvain and Poulain, Pierre and Bertrand, Olivier and Faure, Guilhem and Rebehmed, Joseph and Ghozlane, Amine and Swapna, Lakshmipuram S. and Bhaskara, Ramachandra M. and Barnoud, Jonathan and Téletchéa, Stéphane and Téletchéa, Stéphane and Jallu, Vincent and Cerny, Jiri and Schneider, Bohdan and Etchebest, Catherine and Srinivasan, Narayanaswamy and Gelly, Jean-Christophe and de Brevern, Alexandre G. and Brevern, Alexandre G.}, doi = {10.3389/fmolb.2015.00020}, journal = {Frontiers in Molecular Biosciences}, month = {may}, title = {Protein flexibility in the light of structural alphabets}, url = {http://dx.doi.org/10.3389/fmolb.2015.00020}, volume = {2}, year = {2015} }