SecStrAnnotator:UserManual
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 (assigns them names) 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.
NEWS: SecStrAnnotator 2.0 is now available. There are a few basic differences:
- SecStrAnnotator 2.0 is based on .NET Core, so it is run using .NET Core Runtime (dotnet). This provides (almost) 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!
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.
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 [www.elixir-czech.cz/services].