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Structure of human CYP 2C8 (PDB ID 2nnj) with annotation of the major helices.

SecStrAnnotator is a command line tool for annotation (naming) of secondary structure elements (SSEs), namely helices and β-strands, in protein structures. It is template-based, meaning that a structurally similar template protein with annotated SSEs is a part of the input.

SecStrAnnotator alone can be used for one-to-one annotation. This means that it takes an annotated template protein T and a query protein Q, it finds SSEs in the query protein Q, and annotates the SSEs in a way that best reflects the annotation of the template T.

SecStrAnnotator Suite is a set of additional scripts which can be used for one-to-many annotation. This means that we have a whole protein family, and one of its members serves as the template T. The result is the annotation of all other members of the family. The suite also provides Python and R scripts for a further analysis of the annotation results.

SecStrAPI provides precomputed SSE annotations (currently only for Cytochrome P450 family).


SecStrAnnotator 2 is now available. There are a few basic differences from SecStrAnnotator 1.0:

  • SecStrAnnotator 2 is based on .NET Core and it is run using .NET Core Runtime (dotnet). This provides the same behaviour in each operating system.
  • The supported structural file format is now mmCIF (PDB file format is not supported anymore). Chain and residue numbering is based on label_* columns in the mmCIF files, not auth_* columns!


Annotation of one query protein (one-to-one)

Annotation of a whole protein family (one-to-many)

Analysis of family annotation (case study: Cytochromes P450)



If you found SecStrAnnotator helpful, please cite:

Midlik A, Hutařová Vařeková I, Hutař J, Moturu TR, Navrátilová V, Koča J, Berka K, Svobodová Vařeková R (2019) Automated family-wide annotation of secondary structure elements. In: Kister AE (ed) Protein supersecondary structures: Methods and protocols, Humana Press. ISBN 978-1-4939-9160-0.

Elixirlogo.png SecStrAnnotator Suite is a part of services provided by ELIXIR – European research infrastructure for biological information. For other services provided by ELIXIR's Czech Republic Node visit