Non-synonymous single nucleotide polymorphisms (SNPs) and mutations have been associated with human phenotypes and disease. As more and more SNPs are mapped to phenotypes, understanding how these variations affect the function and expression of genes and gene products becomes an important endeavor. We have developed a set of tools to aid in the understanding of how amino acid substitutions affect protein structures. To do this, we have annotated SNPs in dbSNP and amino acid substitutions in Swiss-Prot with protein structural information, if available. We then developed a novel web interface to this data that allows for visualization of the location of these substitutions. We have also developed a web service interface to the dataset and developed interactive plugins for UCSF's Chimera structural modeling tool and PyMOL that integrate our annotations with these sophisticated structural visualization and modeling tools. The web services portal and plugins can be downloaded from http://www.lifescienceweb.org/ and the web interface is at http://www.mutdb.org/.