# What programs account for structural alignment of different parts of distant homologs which have significant structural differences?

If there is a need to perform structural alignment of different parts of distant homologs, which program one should use?

Since distant homologs often have significant structural changes, meaning the assumption of a similar physico-chemical environment for aligned residues would be violated.

Any program/tools or suggested reference will be a great help.

Thanks.

• You might want to check out TCoffee's Espresso as it does a structure based alignment (requires structures to be given/exist in PDB). However, in my hands it has always performed less than ideally. – Matteo Ferla Sep 14 '20 at 9:05

You can use progressiveMauve (http://darlinglab.org/mauve/user-guide/progressivemauve.html), or bubbz (https://www.cell.com/iscience/fulltext/S2589-0042%2820%2930409-0)