title: PVS: a web server for protein sequence variability analysis tuned to facilitate conserved epitope discovery.
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/.
authors.affiliation: Immunomedicine Group, Department of Microbiology I, Division of Immunology, Facultad de Medicina, Universidad Complutense de Madrid, Ave Complutense s/n, Madrid 28040, Spain.
authors.forename: Maria
authors.initials: M
authors.lastname: Garcia-Boronat
authors.forename: Carmen M
authors.initials: CM
authors.lastname: Diez-Rivero
authors.forename: Ellis L
authors.initials: EL
authors.lastname: Reinherz
authors.forename: Pedro A
authors.initials: PA
authors.lastname: Reche
mesh_terms: D016915:AIDS Vaccines / Q000737:chemistry; D018985:Epitopes, B-Lymphocyte / Q000737:chemistry; D018984:Epitopes, T-Lymphocyte / Q000737:chemistry*; D020407:Internet; D011487:Protein Conformation; D011506:Proteins / Q000276:immunology*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface; D014764:Viral Proteins / Q000737:chemistry
chemical_list: D016915:AIDS Vaccines; D018985:Epitopes, B-Lymphocyte; D018984:Epitopes, T-Lymphocyte; D011506:Proteins; D014764:Viral Proteins