Table 1.
In silico approaches available as online tools.
| Server | Feature | URL | Reference |
|---|---|---|---|
| SIFT | Focuses more on the sequence preservation over the evolutionary time in predicting the effect of residue substitutions on function. | http://sift.bii.a-star.edu.sg/index.html | Kumar et al. (2009), Magesh and Doss (2014) |
| PolyPhen 2.0 | Sequence and structure based method that predicts the possible impact of an amino acid substitution on the structure and function of a protein. | http://genetics.bwh.harvard.edu/pph2 | Adzhubei et al. (2010) |
| I-Mutant 3.0 | Support vector machine (SVM) based predictors of protein stability changes upon single amino acid substitution. | http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant3.0/I-Mutant3.0.cgi | Capriotti et al. (2008) |
| PROVEAN | Sequence based predictor that estimates whether a protein sequence variation affects protein function. | http://provean.jcvi.org | Choi et al. (2012) |
| SNP&GO | Support vector machine (SVM) based web server that combine protein structural/functional parameters and sequence analysis derived information. | http://snps.biofold.org/snps-and-go/snps-and-go.html | Magesh and Doss (2014) |
| PhD-SNP | SVM based on evolutionary information. | http://gpcr.biocomp.unibo.it/cgi/predictors/PhD-SNP/PhD-SNP.cgi | Magesh and Doss (2014) |
| PANTHER | Protein family and subfamily database that predicts the frequency of occurrence of amino acid at a particular position in evolutionary related protein sequences. | http://pantherdb.org/tools/csnpScoreForm.jsp | Mi et al. (2005) |
| UTRscan | Analyzing functional impacts of UTR SNPs. | http://www/.ba.itb.cnr.it/BIG/UTRScan | Pesole et al. (1999) |
| NetSurfP | Analysis of SNP effects on surface and solvent accessibility of protein. | http://www.cbs.dtu.dk/services/NetSurfP | Petersen et al. (2009) |
| I-TASSER | Protein structure prediction server. | http://zhanglab.ccmb.med.umich.edu/I-TASSER | Zhang (2008) |
| HOPE Project | An automatic mutant analysis server for studying the structural features of native protein and the variant models. | http://www.cmbi.ru.nl/hope/home | Venselaar et al. (2010) |
| STRING | Database of known and predicted protein-protein interactions. | http://string-db.org | Von Mering (et al. 2005) |
| PolymiRTS | The polymorphic microRNA target sites are classifies into four classes: ‘D’ (the derived allele disrupts a conserved microRNA site), ‘N’ (the derived allele disrupts a nonconserved microRNA site), ‘C’ (the derived allele creates a new microRNA site) and ‘O’ (other cases when the ancestral allele cannot be determined unambiguously). | http://compbio.uthsc.edu/miRSNP/ | Bhattacharya et al. (2013) |
| 1000 Genomes Project | A resource about human genetic variation that will be used in many studies of particular phenotypes, such as complex diseases or drug response. | http://www.1000genomes.org | Via et al. (2010) |