Computational Structural Biology: Winter 2022

Structure Alignment

Any attempts to study a large collection of objects will usually start with classifying them according to a given measure of similarity. This is probably a consequence of the fact that it is easier to deal with a few representatives than to deal with a whole population. Protein structure similarity is most often detected and quantified by a protein structure alignment program, applied to the different domains of the proteins considered. In this chapter, I review existing techniques for automatically detecting domains in protein structures, as well as techniques for finding the optimal alignment between two structural domains.

Structural alignments of thioredoxins from human and fly. PDB codes 3TRX and 1XWC