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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.

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  • $\begingroup$ 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. $\endgroup$
    – Matteo Ferla
    Commented Sep 14, 2020 at 9:05

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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.

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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)

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