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ProToDeviseR: an automated protein topology scheme generator.
Petar Petrov1, Valerio Izzi2,3
1Infotech Institute, University of Oulu, 90014, Oulu, Finland. petar.petrov@oulu.fi.
BMC Bioinformatics
|March 3, 2025
Summary
Protein topology schemes are essential for proteomics. The Protein Topology Deviser R package (ProToDeviseR) automates the creation of these schemes from various data sources, simplifying protein analysis.
Area of Science:
- Proteomics and Bioinformatics
- Structural Biology
Background:
- Amino acid sequence characterization is crucial for protein analysis.
- Creating clear protein topology schemes is vital for proteomics.
- Integrating data from diverse resources into publication-ready schemes is challenging.
Purpose of the Study:
- To present the Protein Topology Deviser R package (ProToDeviseR).
- To automate the generation of protein topology schemes.
- To provide a user-friendly tool for visualizing protein features.
Main Methods:
- Developed an R package (ProToDeviseR) utilizing R Shiny for a graphical user interface.
- Integrated an enhanced version of Pfam's domains generator for scheme rendering.
- Enabled input from database accession numbers, prediction server results, or manual tables.
Main Results:
- ProToDeviseR automatically generates protein topology schemes.
- The package offers a visually appealing and user-friendly interface.
- It can incorporate data from multiple prediction servers and databases.
Conclusions:
- ProToDeviseR simplifies and accelerates the creation of protein topology schemes.
- The tool efficiently interrogates UniProt and NCBI GenPept databases.
- It elegantly combines features from various data resources for comprehensive analysis.
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