Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-09-18T00:27:19.487Z
Answers.LastActivityDate: 2020-09-18T00:27:19.487Z
Answers.UserDisplayName: user3479780
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-09-19T23:23:57.570Z
Answers.LastActivityDate: 2020-09-19T23:23:57.570Z
Answers.UserDisplayName: jgreener
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-09-14T09:05:56.577Z
Comments.Text: 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.
Comments.UserDisplayName: Matteo Ferla
Tags: <phylogenetics><proteins><protein-structure><3d-structure><structural-biology>
Title: What programs account for structural alignment of different parts of distant homologs which have significant structural differences?
ThreadText: # 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.  
  
  ---
  
  ## 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.
  
  
  ---
  
  ### 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>)
  
  
  ---
  
  