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Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W35-41. doi: 10.1093/nar/gkn211. Epub 2008 Apr 27.

PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery.

Author information

1
Immunomedicine Group, Department of Microbiology I, Division of Immunology, Facultad de Medicina, Universidad Complutense de Madrid, Ave Complutense s/n, Madrid 28040, Spain.

Abstract

We have developed PVS (Protein Variability Server), a web-based tool that uses several variability metrics to compute the absolute site variability in multiple protein-sequence alignments (MSAs). The variability is then assigned to a user-selected reference sequence consisting of either the first sequence in the alignment or a consensus sequence. Subsequently, PVS performs tasks that are relevant for structure-function studies, such as plotting and visualizing the variability in a relevant 3D-structure. Neatly, PVS also implements some other tasks that are thought to facilitate the design of epitope discovery-driven vaccines against pathogens where sequence variability largely contributes to immune evasion. Thus, PVS can return the conserved fragments in the MSA-as defined by a user-provided variability threshold-and locate them in a relevant 3D-structure. Furthermore, PVS can return a variability-masked sequence, which can be directly submitted to the RANKPEP server for the prediction of conserved T-cell epitopes. PVS is freely available at: http://imed.med.ucm.es/PVS/.

PMID:
18442995
PMCID:
PMC2447719
DOI:
10.1093/nar/gkn211
[Indexed for MEDLINE]
Free PMC Article

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