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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
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surfaltr: An R/Bioconductor package to benchmark surface protein isoforms by rapid prediction and visualization of
Pooja Gangras1, Aditi Merchant1,2
1Lilly Institute for Genetic Medicine, Eli Lilly and Company, Indianapolis, Indiana, USA.
Proteomics
|June 9, 2022
Summary
This study introduces surfaltr, an R package for analyzing cell surface protein isoforms. It helps researchers benchmark novel isoforms and prioritize those with diverse transmembrane topologies for therapeutic applications.
Area of Science:
- Biochemistry
- Bioinformatics
- Genomics
Background:
- Cell surface proteins are crucial targets for drug delivery and therapeutic applications.
- Alternative splicing generates diverse protein isoforms with varying subcellular localizations and transmembrane topologies, influencing cell-specific functions.
- Multiomic approaches are identifying novel tissue-specific surface protein isoforms, necessitating efficient bioinformatic tools for analysis.
Purpose of the Study:
- To develop a bioinformatic tool for rapid benchmarking of newly identified cell surface protein isoforms.
- To facilitate the prediction of transmembrane (TM) topologies for user-input isoforms.
- To enable prioritization of topologically diverse isoform pairs for further research.
Main Methods:
- Development of the R package 'surfaltr'.
- Inputting user-defined isoforms and pairing them with known principal isoforms.
- Utilizing TM topology prediction algorithms.
- Incorporating three ranking metrics and protein alignment functions for isoform prioritization.
- Graphical output generation for customizable visualization.
Main Results:
- The 'surfaltr' R package was successfully developed and is available via Bioconductor.
- The package can predict TM topologies and prioritize isoforms based on topological diversity.
- Demonstrated utility by analyzing mouse retina-specific novel surface protein isoforms from prior research.
Conclusions:
- 'surfaltr' addresses the need for efficient bioinformatic benchmarking of surface protein isoforms.
- The package aids in identifying and prioritizing isoforms with significant topological differences.
- Facilitates research into tissue-specific protein isoforms for potential therapeutic development.
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