Difference between revisions of "BIN-SX-Superposition"

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This unit discusses the concepts and practice of structural superposition.
 
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You need to complete the following units before beginning this one:
 
You need to complete the following units before beginning this one:
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*[[BIN-ALI-Alignment]]
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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 ===
 
=== Objectives ===
 
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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.
  
 
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=== Outcomes ===
 
=== Outcomes ===
 
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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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* Browse over the [http://en.wikipedia.org/wiki/Structural_alignment Wikipedia article on '''Structural Superposition'''] <small>(although the article is called "Structural Alignment")</small>.}}
 
* 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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To compute your own superpositions, explore the following tutorials ...
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* ... with '''Chimera''': see [https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/alignments.html '''here'''].
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* ... with '''bio3d''': see [http://thegrantlab.org/bio3d/tutorials/structure-analysis '''here'''] and [http://thegrantlab.org/bio3d/tutorials/principal-component-analysis '''here'''].
  
  
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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
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:2017-08-05
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:2017-10-29
 
<b>Version:</b><br />
 
<b>Version:</b><br />
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:0.1
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:1.0
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
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*1.0 First live version
 
*0.1 First stub
 
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</div>
 
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Revision as of 17:47, 29 October 2017

Structure Superposition


 

Keywords:  Structure superposition and superposition-derived alignment


 



 


 


Abstract

This unit discusses the concepts and practice of structural superposition.


 


This unit ...

Prerequisites

You need to complete the following units before beginning this one:


 


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.


 


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.


 


 


Further reading, links and resources

 


Notes


 


Self-evaluation

 



 



 

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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