Sequence similarity in 3D for comparison of protein families

Homologous proteins are often compared by pairwise sequence alignment, and structure superposition if the atomic coordinates available. Unification of data is an important task in structural biology. Here, we present Sequence Similarity 3D (SS3D) method integrating information. SS3D a distance substitution matrix-based for straightforward visualization regions similarity difference between homologous proteins. This work details approach, demonstrates its utility through case studies comparing members several protein families. The examples show that can effectively highlight biologically dissimilarity. We anticipate will be useful numerous biology applications, including, but not limited to, binding specificity, structure-function relationships, evolutionary pathways. available with manual tutorial at https://github.com/0x462e41/SS3D/.