BIN-SX-Superposition

Structure Superposition

(Structure superposition and superposition-derived alignment)

 

Abstract:

This unit discusses the concepts and practice of structural superposition.

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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.

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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.

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

• BIN-ALI-Alignment (Sequence alignment concepts)
• BIN-SX-Chimera (UCSF ChimeraX: Structure Visualization and Analysis)
• RPR-SX-PDB (Analyzing PDB files)

 

 

 

Evaluation

Evaluation: NA

This unit is not evaluated for course marks.

Contents

Task:

• Read the introductory notes on [http://steipe.biochemistry.utoronto.ca/abc/assets/BIN-SX-Superposition.pdf the optimal superposition of protein 3D structures
• Browse over the Wikipedia article on Structural Superposition (although the article is called "Structural Alignment").]

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.

 

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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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