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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery.
Maria Garcia-Boronat1, Carmen M Diez-Rivero, Ellis L Reinherz
1Immunomedicine Group, Department of Microbiology I, Division of Immunology, Facultad de Medicina, Universidad Complutense de Madrid, Ave Complutense s/n, Madrid 28040, Spain.
The Protein Variability Server (PVS) analyzes protein sequence variability for structure-function studies and vaccine design. It identifies conserved regions and predicts T-cell epitopes, aiding in understanding immune evasion in pathogens.
Area of Science:
- Bioinformatics
- Structural Biology
- Immunology
Background:
- Protein sequence variability is crucial for understanding protein function and immune evasion in pathogens.
- Existing tools may not fully integrate variability analysis with structural visualization and epitope prediction.
Purpose of the Study:
- To develop a web-based tool, the Protein Variability Server (PVS), for comprehensive analysis of protein sequence variability.
- To facilitate structure-function studies and the design of epitope discovery-driven vaccines.
Main Methods:
- PVS computes absolute site variability in multiple protein-sequence alignments (MSAs) using various metrics.
- It assigns variability to a reference sequence and visualizes it on 3D structures.
- PVS identifies conserved fragments based on user-defined thresholds and generates variability-masked sequences for epitope prediction.
Main Results:
- PVS provides site-specific variability metrics for MSAs.
- The tool visualizes variability on 3D protein structures.
- Conserved protein fragments and sequences for T-cell epitope prediction (e.g., for RANKPEP) are generated.
Conclusions:
- PVS is a valuable web-based resource for analyzing protein variability.
- The tool supports structure-function investigations and aids in designing vaccines against variable pathogens by identifying conserved epitopes.
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