Editing SecStrAnnotator:UserManual

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[[File:SecStrAnnotator-annotated-2nnj.png | thumb | right | 400px | 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).


'''[http://sestra.ncbr.muni.cz SecStrAnnotator Online]''' is a web application allowing you to annotate SSEs without installing the full version of SecStrAnnotator.


'''NEWS:'''

'''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 (<code>dotnet</code>). 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!


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===[[SecStrAnnotator:Introduction | Introduction]]===
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===[[SecStrAnnotator:OneToOne | Annotation of one query protein (one-to-one)]]===
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===[[SecStrAnnotator:OneToMany | Annotation of a whole protein family (one-to-many)]]===
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===[[SecStrAnnotator:Analysis | Analysis of family annotation (case study: Cytochromes P450)]]===
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===[[SecStrAnnotator:SecStrAPI | SecStrAPI]]===
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===[[SecStrAnnotator:Download | Download]]===
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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) [https://link.springer.com/protocol/10.1007/978-1-4939-9161-7_3 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.
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| '''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 [https://www.elixir-czech.cz/services www.elixir-czech.cz/services].
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