BIN-SX-Superposition

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:

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

 

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:

• 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").]

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

 

 

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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.

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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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