PON-P2 protocols

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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 in pipelines

 (2)
2017
PMCID: 5525221
PMID: 28738860
DOI: 10.1186/s12885-017-3488-x

[…] by default snps with minor allele frequencies (mafs) > 0.05 []., the effect of the amino-acid changing variant, c.2861 t > g (leu954arg), was predicted using the pathogenic-or-not-pipeline (pon-p2) programme []. the functionality of the observed snps with rs ids was analysed using haploreg v2 [], including conserved region, open chromatin, regulatory chromatin state […]

2015
PMCID: 4539680
PMID: 26282678
DOI: 10.1186/s12920-015-0125-x

[…] in the varibench database (http://structure.bmc.lu.se/varibench/cancer.php). predictions for all aass supporting the results of this article are freely available at http://structure.bmc.lu.se/pon-p2/cancer30.html/., additional file 1: additional file 2: additional file 3: additional file 4: additional file 5: additional file 6: additional file 7: additional file 8: […]


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PON-P2 in publications

 (11)
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 […]

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 […]

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, […]

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 […]

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 […]


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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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