RVP-NET statistics

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Citations per year

Number of citations per year for the bioinformatics software tool RVP-NET
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Tool usage distribution map

This map represents all the scientific publications referring to RVP-NET per scientific context
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Protocols

RVP-NET specifications

Information


Unique identifier OMICS_15444
Name RVP-NET
Interface Web user interface
Restrictions to use None
Input data A protein sequence.
Input format FASTA, TXT, PIR, SWISSPROT
Computer skills Basic
Stability Stable
Maintained No

Maintainer


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Publication for RVP-NET

RVP-NET citations

 (16)
library_books

MDD Palm: Identification of protein S palmitoylation sites with substrate motifs based on maximal dependence decomposition

2017
PLoS One
PMCID: 5491019
PMID: 28662047
DOI: 10.1371/journal.pone.0179529

[…] : 11+e−x [].The structural features of ASA were investigated based on the accessibility of a side-chain of amino acids on the surface of a protein that experienced post-translational modification []. RVP-Net [] was used to calculate the ASA value from the protein sequence because of the lack of most S-palmitoylated protein tertiary structures in PDB []. RVP-Net can predict the real ASA of a residu […]

library_books

Investigation and identification of protein carbonylation sites based on position specific amino acid composition and physicochemical features

2017
BMC Bioinformatics
PMCID: 5374553
PMID: 28361707
DOI: 10.1186/s12859-017-1472-8

[…] translational modification prefers to be accessible on the surface of a protein []. Although the tertiary structures of carbonylated proteins are limited, based on the prediction of ASA values by the RVP-Net tool, ASA was examined as an attribute for the identification of carbonylation sites. To explore how amino acids flanking the carbonylated and non-carbonylated sites might differ in their inte […]

library_books

A hydrophobic spine stabilizes a surface exposed α helix according to analysis of the solvent accessible surface area

2016
BMC Bioinformatics
PMCID: 5259910
PMID: 28155647
DOI: 10.1186/s12859-016-1368-z

[…] A predictors (which are based on Barton502). To compare the predictive models of amino acid residues, the test dataset was also processed using several RSA predictors, including SPINE X [], SABLE [], RVP-net [], and SARpred []. The test results are presented in Table . RSA predictors for Ala, Asp, Asn, Glu, Gln, Gly, Ile, Leu, Ser, and Tyr showed better performance than the predictors correspondin […]

library_books

RF Phos: A Novel General Phosphorylation Site Prediction Tool Based on Random Forest

2016
Biomed Res Int
PMCID: 4811047
PMID: 27066500
DOI: 10.1155/2016/3281590

[…] ot undergo posttranslational modification because they are not expected to interact with the modifying enzymes. Therefore, phosphorylation sites in the protein are expected to be exposed amino acids. Rvp-net [], software for prediction of ASA, was used to extract ASA features from the benchmark protein sequences. ASA features were predicted before dividing the sequences into windows. […]

library_books

SOHSite: incorporating evolutionary information and physicochemical properties to identify protein S sulfenylation sites

2016
BMC Genomics
PMCID: 4895302
PMID: 26819243
DOI: 10.1186/s12864-015-2299-1

[…] lity of an amino acid side-chain on the surface of a protein that experience post-translational modification [], was also included as an attribute for the identification of S-sulfenylation sites. The RVP-Net [, ] was applied to compute the ASA value from the protein sequence due to the lack of experimentally verified tertiary structures of S-sulfenylated protein in the Protein Data Bank (PDB) []. […]

call_split

Characterization and identification of protein O GlcNAcylation sites with substrate specificity

2014
BMC Bioinformatics
PMCID: 4290634
PMID: 25521204
DOI: 10.1186/1471-2105-15-S16-S1
call_split See protocol

[…] lvent-accessible surface area (ASA) was employed. Due to the lack of protein tertiary structures for most O-GlcNAcylated proteins in PDB [], with reference to a previous method [], an effective tool, RVP-Net [,], was applied to compute the ASA value from protein sequence, showing the proportion of the solvent-accessible area for each amino acid on proteins. Briefly, ASA value of all residues came […]


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RVP-NET institution(s)
Department of Biochemical Engineering and Science, Kyushu Institute of Technology, IZUKA, Japan; Computational Biology Research Center (CBRC), AIST, Tokyo, Japan

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