<p>You can use <code>progressiveMauve</code> (<a href="http://darlinglab.org/mauve/user-guide/progressivemauve.html" rel="nofollow noreferrer">http://darlinglab.org/mauve/user-guide/progressivemauve.html</a>), or <code>bubbz</code> (<a href="https://www.cell.com/iscience/fulltext/S2589-0042%2820%2930409-0" rel="nofollow noreferrer">https://www.cell.com/iscience/fulltext/S2589-0042%2820%2930409-0</a>)</p>

CC BY-SA 4.0
2020-09-18T00:27:19.487Z
2020-09-18T00:27:19.487Z
user3479780
<p>TM-align has some options to do this, see for example <a href="https://zhanglab.ccmb.med.umich.edu/TM-align/help.html" rel="nofollow noreferrer">https://zhanglab.ccmb.med.umich.edu/TM-align/help.html</a>.</p>
<p>TM-align is similar to TM-score but the alignment is purely structural.</p>

CC BY-SA 4.0
2020-09-19T23:23:57.570Z
2020-09-19T23:23:57.570Z
jgreener
<p>If there is a need to perform structural alignment of different parts of distant homologs, which program one should use?</p>
<p>Since distant homologs often have significant structural changes, meaning the assumption of a similar physico-chemical environment for aligned residues would be violated.</p>
<p>Any program/tools or suggested reference will be a great help.</p>
<p>Thanks.</p>

CC BY-SA 4.0
2020-09-14T09:05:56.577Z
You _might_ want to check out [TCoffee's Espresso](http://tcoffee.crg.cat/apps/tcoffee/do:expresso) 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
<phylogenetics><proteins><protein-structure><3d-structure><structural-biology>
What programs account for structural alignment of different parts of distant homologs which have significant structural differences?
# What programs account for structural alignment of different parts of distant homologs which have significant structural differences?

(Asked by: username_0 on 2020-09-13)

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.

**Tags:** phylogenetics, proteins, protein-structure, 3d-structure, structural-biology
> **Comments:**
> **username_1**: You _might_ want to check out [TCoffee's Espresso](http://tcoffee.crg.cat/apps/tcoffee/do:expresso) 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.  

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## 2 answers

### Answer by username_3 on 2020-09-19. Score: 1

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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### Answer by username_2 on 2020-09-18. Score: 0

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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