Difference between revisions of "BIN-SX-Superposition"

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<b>Deliverables:</b><br />
 
<b>Deliverables:</b><br />
 
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<section begin=deliverables />
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<li><b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.</li>
 
<li><b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.</li>
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<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
 
<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
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<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
 
<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
 
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<section end=deliverables />
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<section begin=prerequisites />
 
<section begin=prerequisites />
 
<b>Prerequisites:</b><br />
 
<b>Prerequisites:</b><br />
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This unit builds on material covered in the following prerequisite units:<br />
 
This unit builds on material covered in the following prerequisite units:<br />
 
*[[BIN-ALI-Alignment|BIN-ALI-Alignment (Sequence alignment concepts)]]
 
*[[BIN-ALI-Alignment|BIN-ALI-Alignment (Sequence alignment concepts)]]
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*[[BIN-SX-Chimera|BIN-SX-Chimera (UCSF Chimera: Structure Visualization and Analysis)]]
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*[[BIN-SX-Chimera|BIN-SX-Chimera (UCSF ChimeraX: Structure Visualization and Analysis)]]
 
*[[RPR-SX-PDB|RPR-SX-PDB (Analyzing PDB files)]]
 
*[[RPR-SX-PDB|RPR-SX-PDB (Analyzing PDB files)]]
 
<section end=prerequisites />
 
<section end=prerequisites />
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=== Evaluation ===
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<b>Evaluation: NA</b><br />
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<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
 
== Contents ==
 
== Contents ==
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== Notes ==
 
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<references />
 
 
== Further reading, links and resources ==
 
== Further reading, links and resources ==
 
<!-- {{#pmid: 19957275}} -->
 
<!-- {{#pmid: 19957275}} -->
 
<!-- {{WWW|WWW_GMOD}} -->
 
<!-- {{WWW|WWW_GMOD}} -->
 
<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
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== Notes ==
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<references />
  
 
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<b>If in doubt, ask!</b> If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
 
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*0.1 First stub
 
*0.1 First stub
 
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Revision as of 09:27, 25 September 2020

Structure Superposition

(Structure superposition and superposition-derived alignment)


 


Abstract:

This unit discusses the concepts and practice of structural superposition.

Objectives:
This unit will ...

  • ... introduce the concepts of structural superposition;
  • ... demonstrate the outcomes of superpositions in the presence and absence of sigificant sequence similarity;
  • ... point you to servers that allow superposition-based searches for similar proteins
  • ... list tutorials for superposition with Chimera and bio3d.

Outcomes:
After working through this unit you ...

  • ... can discover proteins that are structurally similar to a query;
  • ... can compute a structural superposition with Chimera or bio3d;
  • ... derive a superposition-based alignment.

Deliverables:

  • Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
  • Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
  • Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

    • Prerequisites:
    This unit builds on material covered in the following prerequisite units:


     


    This page is tagged for revision; expect changes and proceed with caution.


     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    Contents

    Task:

    To compute your own superpositions, explore the following tutorials ...

    • ... with Chimera: see here.
    • ... with bio3d: see here and here.


     

    Self-evaluation

    Further reading, links and resources

    Notes


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2017-10-29

    Version:

    1.0

    Version history:

    • 1.0 First live version
    • 0.1 First stub

    CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

    This page is tagged for revision; expect changes and proceed with caution.
    Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=BIN-SX-Superposition&oldid=11702"