Difference between revisions of "BIN-SX-Superposition"

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Structure Superposition
 
Structure Superposition
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(Structure superposition and superposition-derived alignment)
 
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To compute your own superpositions, explore the following tutorials ...
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Put this into practice with ChimeraX:
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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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== Self-evaluation ==
 
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== Further reading, links and resources ==
 
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Revision as of 13:43, 27 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:

    1.1

    Version history:

    • 1.1 Maintenance
    • 1.0 First live version
    • 0.1 First stub

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