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

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No longer maintained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.