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SNPdbe: constructing an nsSNP functional impacts database

C. Schaefer, A. Meier, B. Rost, Y. Bromberg
2011 Bioinformatics  
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

Ruiyang Song, Baixin Cao, Zhenling Peng, Christopher J. Oldfield, Lukasz Kurgan, Ka-Chun Wong, Jianyi Yang
2021 Biomolecules  
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

Fakher Rahim, Hamid Galehdari, Javad Mohammadi-asl, Najmaldin Saki
2013 Genetics Research International  
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

Tugba Kucukkal, Ye Yang, Susan Chapman, Weiguo Cao, Emil Alexov
2014 International Journal of Molecular Sciences  
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]

Yue'e Chen, Wanyun Xu, Chuangfu Chen, Hugh T Blair, Jianfeng Gao
2016 bioRxiv   pre-print
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

Christopher Michael Yates, Michael Sternberg, Medical Research Council (Great Britain)
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