Automated Family-Wide Annotation of Secondary Structure Elements

Midlik, Adam; Vařeková, Ivana Hutařová; Hutař, Jan; Moturu, Taraka Ramji; Navrátilová, Veronika; Koča, Jaroslav; Berka, Karel; Vařeková, Radka Svobodová

doi:10.1007/978-1-4939-9161-7_3

Cited by 5 publications

(10 citation statements)

References 21 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…1a. General methods for the selection and annotation of the template with and without any prior knowledge can be found our earlier publication 20 .…”

Section: Template Annotationmentioning

confidence: 99%

“…The annotation was performed using our software SecStrAnnotator. The current version 2.2 has been improved since the original publication 20 of SecStrAnnotator 1.0, the most significant changes being the support for mmCIF files, label_* numbering, revised secondary structure assignment method (geom-hbond2), and detection of structural irregularities within SSEs. Switching from .NET Framework to .NET Core enabled more consistent usage across operating systems.…”

Section: Annotation Proceduresmentioning

confidence: 99%

“…The annotation algorithm consists of three main steps: secondary structure assignment, structural alignment and SSE matching. Detailed description is provided in Midlik et al 20 . SecStrAnnotator was run with these settings: --ssa geom-hbond2 --align cealign --matching mom --soft --maxmetric 25,0.5,0.5 --label2auth --verbose.…”

Section: Annotation Proceduresmentioning

confidence: 99%

“…Previously, we presented methods for automated annotation of SSEs in protein families, implemented in tool SecStrAnnotator (Midlik et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…Previously, we presented methods for automated annotation of SSEs in protein families, implemented in tool SecStrAnnotator 20 . Automated annotation opens the possibility to focus on any protein family and describe its general SSE anatomy, which can bring a valuable insight to the understanding of its function -SSEs typically present, their occurrence, typical length, position and amino acid composition and variation for individual SSE classes.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

Midlik

Navrátilová

Moturu

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

Motivation:Protein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of homologous structures and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, assigning always the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs and their variability provides an overview of the studied protein family and can be used to enrich the analysis of a particular protein at hand. Results: We developed a workflow for analysis of the secondary structure anatomy of a protein family, based on SSE annotation tool SecStrAnnotator. We applied this analysis to the model family of cytochromes P450 (CYPs)a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, as well as the conservation/variability of these properties. We also suggest a generic residue numbering scheme for the CYP family. The comparison between the bacterial and eukaryotic part of the family highlights the major differences and reveals an anomalous group of bacterial CYPs with some typically eukaryotic features. This hints at possible evolutionary and functional relationships.

show abstract

“…1a. General methods for the selection and annotation of the template with and without any prior knowledge can be found our earlier publication 20 .…”

Section: Template Annotationmentioning

confidence: 99%

Section: Annotation Proceduresmentioning

confidence: 99%

Section: Annotation Proceduresmentioning

confidence: 99%

“…Previously, we presented methods for automated annotation of SSEs in protein families, implemented in tool SecStrAnnotator (Midlik et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

Midlik

Navrátilová

Moturu

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

A novel dual three and five-component reactions between dimedone, aryl aldehydes, and 1-naphthylamine: synthesis and computational studies

Langarizadeh

Eskandari

Abiri

et al. 2022

Journal of Molecular Structure

View full text Add to dashboard Cite

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

Midlik

Navrátilová

Moturu

et al. 2021

Sci Rep

Self Cite

View full text Add to dashboard Cite

Protein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of structures, and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, always assigning the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs provides an overview of the studied family and enriches the analysis of any particular protein at hand. We developed a workflow for the analysis of the secondary structure anatomy of a protein family. We applied this analysis to the model family of cytochromes P450 (CYPs)—a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, the conservation/variability of these properties and relationship to the substrate recognition sites. We also suggest a generic residue numbering scheme for the CYP family. Comparing the bacterial and eukaryotic part of the family highlights the significant differences and reveals a well-known anomalous group of bacterial CYPs with some typically eukaryotic features. Our workflow for SSE annotation for CYP and other families can be freely used at address https://sestra.ncbr.muni.cz.

show abstract

Automated Family-Wide Annotation of Secondary Structure Elements

Cited by 5 publications

References 21 publications

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

A novel dual three and five-component reactions between dimedone, aryl aldehydes, and 1-naphthylamine: synthesis and computational studies

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

Contact Info

Product

Resources

About