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.

Introduction

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

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

Download

How to cite

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.