text: user3656: 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.
  
  user4622: 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.
  
original_text: 3656: <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>
   4622: <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>
  