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Protocols

PON-P2 specifications

Information


Unique identifier OMICS_12153
Name PON-P2
Interface Web user interface
Restrictions to use None
Input data Some protein/gene identifier(s) and variation(s).
Computer skills Basic
Stability Stable
Registration required Yes
Maintained Yes

Maintainer


  • person_outline Mauno Vihinen <>

Publication for PON-P2

PON-P2 citations

 (11)
library_books

Development of pathogenicity predictors specific for variants that do not comply with clinical guidelines for the use of computational evidence

2017
PMCID: 5558188
PMID: 28812538
DOI: 10.1186/s12864-017-3914-0

[…] from 228 proteins to identify those cases for which pathogenicity predictors disagree. we have repeated this process for all the possible combinations of five known methods (sift, polyphen-2, pon-p2, cadd and mutationtaster2). for each resulting subset we have trained a specific pathogenicity predictor. we find that these specific predictors are able to discriminate between neutral […]

library_books

Germline EMSY sequence alterations in hereditary breast cancer and ovarian cancer families

2017
PMCID: 5525221
PMID: 28738860
DOI: 10.1186/s12885-017-3488-x

[…] with a positively charged arginine at position 954. the heterozygous rs184345272 variant was identified in two patients (2 of 106, 1.9%) and three controls (3 of 376, 0.8%) (or = 2.40; p = 0.3). pon-p2 predicts the unknown effects of substitutions., the most interesting finding was the rare novel sequence alteration, c.2709 + 122delt (fig. ). the precise location of the deleted t could […]

library_books

Variants of the ABCA3 gene might contribute to susceptibility to interstitial lung diseases in the Chinese population

2017
PMCID: 5481373
PMID: 28642621
DOI: 10.1038/s41598-017-04486-y

[…] p.a678t) was in nbd1. the distribution of the thirteen missense variants in abca3 is shown in fig. .figure 1 , we then applied three of the variants prediction algorithms, i.e., sift, polyphen and pon-p2, which use different parameters, to assess the functional damage arising from the detected thirteen missense variants. seven of the missense variants (p.l39v, p.l290q, p.a678t, p.e793k, […]

library_books

In silico analyses of deleterious missense SNPs of human apolipoprotein E3

2017
PMCID: 5449402
PMID: 28559539
DOI: 10.1038/s41598-017-01737-w

[…] (sdm), fold-x and popmusic., in order to obtain a consensus score based on many different snp impact prediction strategies, the following types of consensus software were used: condel, meta-snp, pon-p2 and predictsnp, ., the consurf server is a tool for estimating the evolutionary conservation of amino acid positions in a protein molecule based on the phylogenetic relations […]

library_books

The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer

2016
PMCID: 5156680
PMID: 28018905
DOI: 10.3389/fmolb.2016.00078

[…] effects of mutations was carried out using different sequence-based methods. specifically, we integrated provean (choi et al., ), mutation assessor (reva et al., ), polyphen2 (adzhubei et al., ), pon-p2 (niroula et al., ), snap2 (bromberg et al., ), aligngvgd (tavtigian, ; mathe et al., ), and mutpred (li et al., ). each method had different threshold values to discriminate between pathogenic […]

library_books

Recurrent HOXB13 mutations in the Dutch population do not associate with increased breast cancer risk

2016
PMCID: 4948019
PMID: 27424772
DOI: 10.1038/srep30026

[…] were predicted to be deleterious based on three different prediction classification tools: predictsnp (i.e. 87% for p.g84e and p.r217c), meta-snp (i.e. 0.730 for p.g84e and 0.895 for p.r217c) and pon-p2 (i.e. 0.967 for p.g84e and 0.974 for p.r217c). moreover, p.g84e is localized in the meis binding domain, whereas p.r217c is localized to the homeodomain of hoxb13, further increasing […]


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PON-P2 institution(s)
Department of Experimental Medical Science, Lund University, Lund, Sweden
PON-P2 funding source(s)
Partly supported by the Faculty of Medicine, Lund University and from Vetenskapsradet.

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