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A tremendous number of protein structures is available in the Protein Data Bank (PDB) nowadays. Similar structures can be grouped together in so called protein families. As more and more structures are being collected in each family, the protein families have become very rich datasets. Based on these data, we can reach key research results – from understanding biomacromolecular functions and mechanisms of their action to the classification of types of diseases or the rational development of novel drugs.

But first we must me able to orient within the collected data. Secondary structure elements (SSEs), mainly helices and β-strands, are inherent parts of protein structures and their arrangement is characteristic for each protein family – they are something like bones in an animal body. Therefore, identification and annotation (naming) of the SSEs can facilitate orientation in the vast number of structures in each protein family. Annotated SSEs can be used as a reference to describe the position of the key regions (active sites, channel etc.), as tools to characterize the general anatomy of a family or to compare its members, and their relation to the protein function can be studied.

SecStrAnnotator is a tool which can be used for automated annotation of SSEs within protein families. It means that it assigns names to the SSEs in such way that the equivalent SSEs in each member of the family have the same name.

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