Difference between revisions of "BIN-SX-Superposition"

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<div id="ABC">
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
Structure Superposition
 
Structure Superposition
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  </div>
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
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(Structure superposition and superposition-derived alignment)
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  {{Vspace}}
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</div>
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
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Structure superposition and superposition-derived alignment
 
 
</div>
 
</div>
  
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{{Smallvspace}}
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__TOC__
 
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{{Vspace}}
 
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{{DEV}}
 
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{{Vspace}}
 
  
  
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
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<div style="font-size:118%;">
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<b>Abstract:</b><br />
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<section begin=abstract />
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This unit discusses the concepts and practice of structural superposition.
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<section end=abstract />
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</div>
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<!-- ============================  -->
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<hr>
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<table>
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<tr>
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<td style="padding:10px;">
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<b>Objectives:</b><br />
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This unit will ...
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* ... introduce the concepts of structural superposition;
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* ... demonstrate the outcomes of superpositions in the presence and absence of sigificant sequence similarity;
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* ... point you to servers that allow superposition-based searches for similar proteins
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* ... list tutorials for superposition with Chimera and bio3d.
 +
</td>
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<td style="padding:10px;">
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<b>Outcomes:</b><br />
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After working through this unit you ...
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* ... can discover proteins that are structurally similar to a query;
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* ... can compute a structural superposition with Chimera or bio3d;
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* ... derive a superposition-based alignment.
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</td>
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</tr>
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</table>
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<!-- ============================  -->
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<hr>
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<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>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>
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<section end=deliverables />
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<!-- ============================  -->
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<hr>
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<section begin=prerequisites />
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<b>Prerequisites:</b><br />
 +
This unit builds on material covered in the following prerequisite units:<br />
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*[[BIN-ALI-Alignment|BIN-ALI-Alignment (Sequence alignment concepts)]]
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*[[BIN-SX-Chimera|BIN-SX-Chimera (UCSF ChimeraX: Structure Visualization and Analysis)]]
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*[[RPR-SX-PDB|RPR-SX-PDB (Analyzing PDB files)]]
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<section end=prerequisites />
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<!-- ============================  -->
 
</div>
 
</div>
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<div id="ABC-unit-framework">
 
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== Abstract ==
 
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<!-- included from "../components/BIN-SX-Superposition.components.wtxt", section: "abstract" -->
 
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...
 
  
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{{Smallvspace}}
  
  
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== This unit ... ==
 
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=== Prerequisites ===
 
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<!-- included from "../components/BIN-SX-Superposition.components.wtxt", section: "prerequisites" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
 
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You need to complete the following units before beginning this one:
 
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*[[BIN-ALI-Alignment]]
 
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*[[BIN-SX-Chimera]]
 
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*[[RPR-SX-PDB]]
 
  
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{{Vspace}}
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{{Smallvspace}}
  
  
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=== Objectives ===
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__TOC__
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<!-- included from "../components/BIN-SX-Superposition.components.wtxt", section: "objectives" -->
 
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...
 
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=== Outcomes ===
 
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<!-- included from "../components/BIN-SX-Superposition.components.wtxt", section: "outcomes" -->
 
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...
 
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=== Deliverables ===
 
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<!-- included from "../components/BIN-SX-Superposition.components.wtxt", section: "deliverables" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" -->
 
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*<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.
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
 
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*<b>Journal</b>: Document your progress in your [[FND-Journal|course journal]].
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
 
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*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|insights! page]].
 
  
 
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=== Evaluation ===
 
=== Evaluation ===
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<!-- included from "../components/BIN-SX-Superposition.components.wtxt", section: "evaluation" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "eval-none" -->
 
 
<b>Evaluation: NA</b><br />
 
<b>Evaluation: NA</b><br />
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:This unit is not evaluated for course marks.
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<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
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<div id="BIO">
 
 
== Contents ==
 
== Contents ==
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<!-- included from "../components/BIN-SX-Superposition.components.wtxt", section: "contents" -->
 
  
 
{{Task|1=
 
{{Task|1=
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* Read the introductory notes on {{ABC-PDF|BIN-SX-Superposition|the optimal superposition of protein 3D structures
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* Read the introductory notes on {{ABC-PDF|BIN-SX-Superposition|the optimal superposition of protein 3D structures}}
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* Browse over the [http://en.wikipedia.org/wiki/Structural_alignment Wikipedia article on '''Structural Superposition'''] <small>(although the article is called "Structural Alignment")</small>.}}
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* Browse over the [http://en.wikipedia.org/wiki/Structural_alignment Wikipedia article on '''Structural Superposition'''] <small>(although the article is called "Structural Alignment")</small>.
 
}}
 
}}
  
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Put this into practice with ChimeraX:
  
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{{Vspace}}
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{{ABC-unit|RPR-ChimeraX_remote.R}}
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== Further reading, links and resources ==
 
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<!-- {{#pmid: 19957275}} -->
 
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<!-- {{WWW|WWW_GMOD}} -->
 
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<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
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== Notes ==
 
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<!-- included from "../components/BIN-SX-Superposition.components.wtxt", section: "notes" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "notes" -->
 
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<references />
 
  
 
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== Self-evaluation ==
 
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<!-- included from "../components/BIN-SX-Superposition.components.wtxt", section: "self-evaluation" -->
 
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=== Question 1===
 
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Question ...
 
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Answer ...
 
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Answer ...
 
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----
 
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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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<div class="about">
 
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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
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:2017-08-05
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:2020-09-26
 
<b>Version:</b><br />
 
<b>Version:</b><br />
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:0.1
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:2.0
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
 +
*2.0 Move core of the Chimera practice into a Chimera remote-control script
 +
*1.0 First live version
 
*0.1 First stub
 
*0.1 First stub
 
</div>
 
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[[Category:ABC-units]]
 
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{{CC-BY}}
 
{{CC-BY}}
  
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[[Category:ABC-units]]
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{{UNIT}}
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Latest revision as of 06:57, 28 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:


     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    Contents

    Task:

    Put this into practice with ChimeraX:

    Task:

     
    • Open RStudio and load the ABC-units R project. If you have loaded it before, choose File → Recent projects → ABC-Units. If you have not loaded it before, follow the instructions in the RPR-Introduction unit.
    • Choose Tools → Version Control → Pull Branches to fetch the most recent version of the project from its GitHub repository with all changes and bug fixes included.
    • Type init() if requested.
    • Open the file RPR-ChimeraX_remote.R and follow the instructions.


     

    Note: take care that you understand all of the code in the script. Evaluation in this course is cumulative and you may be asked to explain any part of code.


     


     


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-09-26

    Version:

    2.0

    Version history:

    • 2.0 Move core of the Chimera practice into a Chimera remote-control script
    • 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.

    Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=BIN-SX-Superposition&oldid=11787"