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SNPdbe: constructing an nsSNP functional impacts database
2011
Bioinformatics
Preserved Fulltext
Here, we introduce SNPdbe-SNP database of effects, with predictions of computationally annotated functional impacts of SNPs. ...
Most polymorphisms lack experimental annotation of their functional impact. ...
ACKNOWLEDGEMENTS We thank to Laszlo Kajan, Guy Yachdav and Tim Karl (TUM) for maintenance of our compute cluster and to those who deposit their experimental data in public databases. ...
doi:10.1093/bioinformatics/btr705
pmid:22210871
pmcid:PMC3278761
fatcat:slwoanrpmzczffkd2khqzypth4
Accurate Sequence-Based Prediction of Deleterious nsSNPs with Multiple Sequence Profiles and Putative Binding Residues
2021
Biomolecules
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Non-synonymous single nucleotide polymorphisms (nsSNPs) may result in pathogenic changes that are associated with human diseases. Accurate prediction of these deleterious nsSNPs is in high demand. ...
In particular, DMBS secures AUC = 0.97 for the SNPdbe and ExoVar datasets, compared to AUC = 0.70 and 0.88, respectively, that were obtained by the best available methods. ...
Data Availability Statement: The data presented in this study are available in [13] (HumVar and HumDiv) [9] (SNPdbe), and [15] (ExoVar). ...
doi:10.3390/biom11091337
pmid:34572550
pmcid:PMC8469993
fatcat:dpj7tnpw75eydcbm2nuylyu7eq
Regression Modeling and Meta-Analysis of Diagnostic Accuracy of SNP-Based Pathogenicity Detection Tools forUGT1A1Gene Mutation
2013
Genetics Research International
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Although the accuracy of our suggested model is not relatively high, the functional impact of the pathogenic mutations is highlighted at the protein level, which improves the understanding of the molecular ...
This review summarized all available evidence on the accuracy of SNP-based pathogenicity detection tools and introduced regression model based on functional scores, mutation score, and genomic variation ...
causes inactivation of the enzyme you could perform an in vitro functional study by cloning the mutated cDNA of UGT1A1 in an expression vector. ...
doi:10.1155/2013/546909
pmid:23997956
pmcid:PMC3753762
fatcat:fxg72xx3qrhjnb2q642re745fq
Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics
2014
International Journal of Molecular Sciences
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DNA mutations are the cause of many human diseases and they are the reason for natural differences among individuals by affecting the structure, function, interactions, and other properties of DNA and ...
Statistical Potentials The statistical potential energy functions are an alternative to the energy functions delivered from first principles, i.e., biophysics-based energy functions. ...
A site-direct mutation caused by an nsSNP can alter both the secondary structural element and the bond rotations and can be evaluated by CD spectrum, by comparison with fully functional wild-type protein ...
doi:10.3390/ijms15069670
pmid:24886813
pmcid:PMC4100115
fatcat:wvilvvfkmfbz3owuys6qjz4npq
Variations in MHC-DRB1 exon2 and associations with Brucellosis susceptibility in Chinese Merino sheep
[article]
2016
bioRxiv
pre-print
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SNPdbe: constructing an nsSNP 292 functional impacts database. Bioinformatics. 28:601-602. 293 Yang, S., H.S. Ge, A.P. Zhang, S.C. Wei, M. Gao, H.Y. Wang, J.J. Chen, M. Li, Y.H. Liang, 294 and P.P. ...
The ovine DRB1 locus is located in the MHC Class II region, and its function is to 49 present extracellular-derived peptides to the immune system. ...
doi:10.1101/038539
fatcat:ive7g7rfzrdohcjrcxe3vbrocm
Analysis and prediction of the effects of single amino acid variants in human disease
2017
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Finally, knowing a variant is potentially damaging to a protein's function does not tell a researcher whether or not it will cause the disease of interest,and even healthy human exomes contain many SAVs ...
This enables researchers to determine which SAVs across an entire exome are likely to be involved in their specific disease of interest. ...
The front-end has been constructed using HTML and uses Perl CGI scripts to either run SuSPect or retrieve pre-calculated scores from an SQLite database using the Perl DBI module. ...
doi:10.25560/44953
fatcat:bc6pz3z2vfhftk74sw5jh4vpe4