Difference between revisions of "BIN-SX-Superposition"

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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 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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<b>Keywords:</b>&nbsp;
 
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Structure superposition and superposition-derived alignment
 
 
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__TOC__
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<b>Abstract:</b><br />
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== Abstract ==
 
 
<section begin=abstract />
 
<section begin=abstract />
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<!-- included from "./components/BIN-SX-Superposition.components.txt", section: "abstract" -->
 
 
This unit discusses the concepts and practice of structural superposition.
 
This unit discusses the concepts and practice of structural superposition.
 
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<section end=abstract />
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<!-- ============================ -->
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== This unit ... ==
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=== Prerequisites ===
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<!-- included from "./components/BIN-SX-Superposition.components.txt", section: "prerequisites" -->
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<b>Objectives:</b><br />
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You need to complete the following units before beginning this one:
 
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*[[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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*[[RPR-SX-PDB|RPR-SX-PDB (Analyzing PDB files)]]
 
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=== Objectives ===
 
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<!-- included from "./components/BIN-SX-Superposition.components.txt", section: "objectives" -->
 
 
This unit will ...
 
This unit will ...
 
* ... introduce the concepts of structural superposition;
 
* ... introduce the concepts of structural superposition;
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* ... point you to servers that allow superposition-based searches for similar proteins
 
* ... point you to servers that allow superposition-based searches for similar proteins
 
* ... list tutorials for superposition with Chimera and bio3d.
 
* ... list tutorials for superposition with Chimera and bio3d.
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<b>Outcomes:</b><br />
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=== Outcomes ===
 
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<!-- included from "./components/BIN-SX-Superposition.components.txt", section: "outcomes" -->
 
 
After working through this unit you ...
 
After working through this unit you ...
 
* ... can discover proteins that are structurally similar to a query;
 
* ... can discover proteins that are structurally similar to a query;
 
* ... can compute a structural superposition with Chimera or bio3d;
 
* ... can compute a structural superposition with Chimera or bio3d;
 
* ... derive a superposition-based alignment.
 
* ... derive a superposition-based alignment.
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<!-- ============================ -->
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=== Deliverables ===
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<b>Deliverables:</b><br />
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<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-time_management" -->
 
*<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.
 
*<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 "./data/ABC-unit_components.txt", section: "deliverables-insights" -->
 
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
*<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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<section begin=prerequisites />
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<b>Prerequisites:</b><br />
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<!-- included from "./data/ABC-unit_components.txt", section: "notes-prerequisites" -->
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This unit builds on material covered in the following prerequisite units:
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*[[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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*[[RPR-SX-PDB|RPR-SX-PDB (Analyzing PDB files)]]
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== Contents ==
 
== Contents ==
 
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== Further reading, links and resources ==
 
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<!-- <div class="reference-box">[http://www.ncbi.nlm.nih.gov]</div> -->
 
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== Notes ==
 
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== Self-evaluation ==
 
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<references />
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== Further reading, links and resources ==
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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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Revision as of 19:32, 26 January 2018

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:


 



 



 


Contents

Task:

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

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


 

Self-evaluation

Notes

Further reading, links and resources

 



 

If in doubt, ask! 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.


 

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

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