SNPs3D protocols

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Associated diseases

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SNPs3D specifications

Information


Unique identifier OMICS_00163
Name SNPs3D
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for SNPs3D

SNPs3D in pipelines

 (5)
2016
PMCID: 4773746
PMID: 26901225
DOI: 10.3390/cancers8020023

[…] was performed using stata software (version 10, stata corp, college station, tx, usa)., haploreg [] was used for functional annotations of candidate snps. polyphen-2 [], snpeffect [], sift [] and snps3d [] were used to predict the function of missense variant on protein function. vegas was used to perform gene-based tests, which produces a gene-based test statistic based on a simulation […]

2015
PMCID: 4556460
PMID: 26322636
DOI: 10.1371/journal.pone.0136379

[…] variant, pairwise ld was assessed using haploview []., we used the function snp prediction (funcpred) pipeline in snpnfo [] that incorporates several software tools/web servers such as polyphen [], snps3d[], match[], and esefinder [] to assess the possibility that snps affect biological function (i.e. protein structure/stability, exon splicing, transcription, etc.)., there were no significant […]

2013
PMCID: 3563522
PMID: 23343470
DOI: 10.1186/1471-2350-14-12

[…] the entire process is presented schematically in figure ., we used different web based tools namely sift (http://sift.jcvi.org), polyphen (http://coot.embl.de/polyphen/), snps3d (http://www.snps3d.org/), pupasuite 2 (http://pupasuite.bioinfo.cipf.es), globplot, fastsnp (http://fastsnp.ibms.sinica.edu.tw), [email protected] (http://variome.kobic.re.kr/snpatpromoter), […]

2013
PMCID: 3674993
PMID: 23754948
DOI: 10.1371/journal.pgen.1003500

[…] to affect protein function. (ii) we used snpinfo to investigate predicted and putative function in several functional classes, including splicing regulation, stop codons, polyphen predictions, snps3d predictions, transcription factor binding site (tfbs) prediction, and mirna binding site prediction., we examined transcript expression of genes near each of the seven identified snp. […]

2011
PMCID: 3500169
PMID: 21504866
DOI: 10.1186/1479-7364-5-3-141

[…] wide range of results, with some databases having extensive links (eg genecards), while others had very few., *indicates link available., aadditional links specific to mutdb: sift; polyphen; ls-snp; snps3d; polydoms; panther; pmut; snpeffect; fastsnp., badditional links specific to genecards: geneloc; dbsnp; aks; huge; aceview; eugenes; mirbase; ecgene; h-invdb; atlas; horde; imgt; leiden; […]


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SNPs3D in publications

 (78)
PMCID: 5942392
PMID: 29765251
DOI: 10.2147/CMAR.S162105

[…] splicing changes are thought to contribute to cancer onset and progression.– these splicing changes induce a nonsynonymous mutation at the rs671 site. the protein coding tools polyphen, sift, and snps3d predicted probable damaging effects to the rs671 site. therefore, we hypothesized that mutation to the rs671 site would induce changes in splicing and protein coding that may serve […]

PMCID: 5817168
PMID: 29511491
DOI: 10.22038/ijbms.2018.25175.6236

[…] first human autophagy-dedicated database. the autophagy genes list, containing lc3, was used as test genes set to find lc3 priority among them in gastric cancer. for training gene set, we used the snps3d server (http://www.snps3d.org/) to get the list of candidate genes associated with gastric cancer. after that, prioritizing servers: toppnet (https://toppgene.cchmc.org/network.jsp), […]

PMCID: 5749718
PMID: 29293570
DOI: 10.1371/journal.pone.0189366

[…] [] (http://provean.jcvi.org/index.php), (4) polyphen-2 [] (http://genetics.bwh.harvard.edu/pph2/), (5) panther [], (6) snps&go [] (http://snps-and-go.biocomp.unibo.it/snps-and-go/), and (7) snps3d [] (http://www.snps3d.org/). mutation assessor [] calculates a functional impact (fi) score for a protein mutation. a functional impact (fi) score ≤ 0.8, 0.8–1.9, 1.9–3.5 and > 3.5 […]

PMCID: 5623905
PMID: 28945216
DOI: 10.1038/oncsis.2017.79

[…] performance, with methods developed specifically for cancer not outperforming general-purpose tools. in an analysis of mutations in two somatic cancer samples, one of the general-purpose tools, snps3d, has predicted a majority of mutations to have a high functional impact. the same tool has been recently applied to interpret potential high-risk alleles in complex human disorders in loci […]

PMCID: 5549357
PMID: 28789679
DOI: 10.1186/s12920-017-0286-x

[…] disease name for gene prioritization. under these conditions we found 12 methods: biograph [], candid [], glad4u [], polysearch [], cipher [], guildify [], disgenet [], geneprospector [], genie [], snps3d [], genedistiller [] and metaranker []. the following methods: cipher, guildify and disgenet were not selected from the prioritization portal but from literature, however, fulfilling […]


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SNPs3D institution(s)
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Chinakville, MD, USA
SNPs3D funding source(s)
This work was supported in part by NLM grant R01 LM07174.

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