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.
TM-align has some options to do this, see for example https://zhanglab.ccmb.med.umich.edu/TM-align/help.html.
TM-align is similar to TM-score but the alignment is purely structural.