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

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 userprovided 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 predicti...

• Type: Journal
• Year: 2008
• Where: NAR
• Authors: Maria Garcia-Boronat, Carmen M. Diez-Rivero, Ellis L. Reinherz, Pedro A. Reche
• Keywords: Absolute Site Variability, NAR 2008, Protein Variability Server, Variability Metrics