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If there is a need to align structurally different parts of distant homologs, which program one should use?

Since distant homologs often have significant structural changes, does that means 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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    $\begingroup$ Try the bioinformatics SE, that is just the sort of question they answer. $\endgroup$ – Polypipe Wrangler Sep 12 '20 at 12:11

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