Dataset Information

2DProts: Database of Family-Wide Protein Secondary Structure Diagrams.

ABSTRACT:

Summary

Secondary structures provide a deep insight into the protein architecture. They can serve for comparison between individual protein family members. The most straightforward way how to deal with protein secondary structure is its visualization using 2 D diagrams. Several software tools for the generation of 2 D diagrams were developed. Unfortunately, they create 2 D diagrams based on only a single protein. Therefore, 2 D diagrams of two proteins from one family markedly differ. For this reason, we developed the 2DProts database, which contains secondary structure 2 D diagrams for all domains from the CATH and all proteins from PDB databases. These 2 D diagrams are generated based on a whole protein family, and they also consider information about the 3 D arrangement of secondary structure elements. Moreover, 2DProts database contains multiple 2 D diagrams, which provide an overview of a whole protein family's secondary structures. 2DProts is updated weekly and is integrated into CATH.

Availability and implementation

Freely accessible at https://2dprots.ncbr.muni.cz. The web interface was implemented in JavaScript. The database was implemented in Python.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Hutarova Varekova I

PROVIDER: S-EPMC8652034 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

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Publications

2DProts: database of family-wide protein secondary structure diagrams.

Hutařová Vařeková Ivana I Hutař Jan J Midlik Adam A Horský Vladimír V Hladká Eva E Svobodová Radka R Berka Karel K

Bioinformatics (Oxford, England) 20211201 23

<h4>Summary</h4>Secondary structures provide a deep insight into the protein architecture. They can serve for comparison between individual protein family members. The most straightforward way how to deal with protein secondary structure is its visualization using 2D diagrams. Several software tools for the generation of 2D diagrams were developed. Unfortunately, they create 2D diagrams based on only a single protein. Therefore, 2D diagrams of two proteins from one family markedly differ. For th ...[more]

PMID: 34244700

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