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Protocols

PVS specifications

Information


Unique identifier OMICS_21155
Name PVS
Alternative name Protein Variability Server
Interface Web user interface
Restrictions to use None
Input data A protein alignment.
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Pedro Reche

Publication for Protein Variability Server

PVS citations

 (29)
library_books

Circulatory white spot syndrome virus in South West region of Bangladesh from 2014 to 2017: molecular characterization and genetic variation

2018
PMCID: 5818386
PMID: 29460184
DOI: 10.1186/s13568-018-0553-z

[…] sh originated isolates. BioEdit Sequence Alignment Editor v7.2.5 (Hall ) was used for a better visualization of the mutations with the position keeping all the sequences altogether in a single frame. Protein Variability server (PVS) (Garcia-Boronat et al. ) was used for finding out protein variability index using the Wu-Kabat variability coefficient of the aligned protein sequences (Kabat et al. ) […]

library_books

Genome Wide Mapping of Peptidases in Rhodnius prolixus: Identification of Protease Gene Duplications, Horizontally Transferred Proteases and Analysis of Peptidase A1 Structures, with Considerations on Their Role in the Evolution of Hematophagy in Triatominae

2017
Front Physiol
PMCID: 5736985
PMID: 29326597
DOI: 10.3389/fphys.2017.01051

[…] rowser at the Vector Base site (https://www.vectorbase.org/organisms/rhodnius-prolixus). Shannon entropy indexes were calculated for multiple protein sequence alignments using the tool present at the Protein Variability Server (at http://imed.med.ucm.es/PVS/, Garcia-Boronat et al., ).We predicted putative glycosylation sites in protein sequences using the tools NetNGlyc (at http://www.cbs.dtu.dk/s […]

library_books

Prevalence of human pegivirus 1 and sequence variability of its E2 glycoprotein estimated from screening donors of fetal stem cell containing material

2017
Virol J
PMCID: 5580293
PMID: 28859680
DOI: 10.1186/s12985-017-0837-y

[…] eotide sequences and count the number of synonymous and nonsynonymous substitutions per site (the ClustalW algorithm with default parameters). Shannon entropy profile was constructed with help of the Protein Variability Server (http://imed.med.ucm.es/PVS; accessed 02.01.2017) []. Secondary structure elements were predicted using the MLRC method [] at the Network Protein Sequence Analysis WWW serve […]

library_books

Designing Epitope Ensemble Vaccines against TB by Selection: Prioritizing Antigens using Predicted Immunogenicity

2017
Bioinformation
PMCID: 5602288
PMID: 28943726
DOI: 10.6026/97320630013220

[…] rotein). To reduce bias, 10 sequences with high coverage and low identity were used to generate multiple sequence alignments. Sequence variability of the resulting alignments was calculated using the Protein Variability Server (PVS; URL: http://imed.med.ucm.es/PVS/), with a minimum fragment length of 9 and a variability threshold of 0.5. Class I and Class II binding profiles were calculated using […]

library_books

Integrity of immunoglobulin variable regions is supported by GANP during AID induced somatic hypermutation in germinal center B cells

2017
Int Immunol
PMCID: 5890899
PMID: 28541550
DOI: 10.1093/intimm/dxx032

[…] (http://www.ebi.ac.uk/Tools/st/emboss_transeq/). The sequences were prepared in the FASTA format and aligned as described above. The aligned sequences were analyzed for protein variability using the Protein Variability Server (PVS) implementing Shannon entropy () (http://imed.med.ucm.es/PVS). […]

library_books

The recombination dynamics of Staphylococcus aureus inferred from spA gene

2016
BMC Microbiol
PMCID: 4940709
PMID: 27400707
DOI: 10.1186/s12866-016-0757-9

[…] grand average of hydropathicity - GRAVY and aliphatic index - AI) were inferred with Compute pI/Mw tool and ProtParam tool, respectively, both available at SIB Bioinformatics Resource Portal []. The Protein Variability Server was used to determine the sequence variability within SpA isoforms using several variability metrics, namely Shannon Entropy, Simpson Diversity Index and Wu-Kabat Variabilit […]

Citations

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PVS institution(s)
Immunomedicine Group, Department of Microbiology I, Division of Immunology, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain; Laboratory of Immunobiology and Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
PVS funding source(s)
Supported by a Ramon y Cajal Grant (‘convocatoria 2005’) and by grant SAF2006-07879 from the ‘Ministerio de Educacio´n y Ciencia’ of Spain.

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