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Table 1 List of databases related to SNPs effect analysis and visualization

From: PSnpBind: a database of mutated binding site protein–ligand complexes constructed using a multithreaded virtual screening workflow

Database Last update Comment
MSV3d [14] 2016, Not downloadable, (web only) Mutated structures built using MODELLER. The website also contains conservation and physio-chemical changes. SwissVar and dbSNP are the main sources of SNPs
PinSnps [15] 2013 Exploring the impact of SNPs on Protein Domains and Complexes
LS-SNP/PDB [16] 2009, Not available anymore  
G23D [17] 2016, Not downloadable, (web only) Used software: SCCCOMP and SCWRL for Side chain modeling, JSmol for molecular graphics, I-mutant and FoldX for thermostability prediction
SNPs3D [18] 2008, Not downloadable SNP impact on protein structure and function. A Support Vector Machine (SVM) model was used to find the separation pattern between a set of diseases and non-deleterious SNPs. The resulting pattern was then validated using a different set of diseases and non-deleterious SNPs.
SAAPdb [19] No longer maintained A newer project SAAPdap/SAAPpred is available - analysis pipeline for examining the structural effects of mutations/prediction of pathogenicity.
SNP2Structure [20] Not available anymore  
PhyreRisk [24] 2019, Not downloadable (web only) A dynamic web application to bridge genomics, proteomics and 3D structural data to guide interpretation of human genetic variants.
toposnp [21] 2019, Databases are up to date, Not downloadable, (web only) Topographic mapping of Single Nucleotide Polymorphism
coliSNP [22] Not available anymore  
StructMAn [23] 2016, Not downloadable (web only) Annotation of non-synonymous single-nucleotide polymorphisms (nsSNPs) in the context of the structural neighbourhood of the resulting amino acid variations in the protein.