BIN-SX-Superposition
Structure Superposition
Keywords: Structure superposition and superposition-derived alignment
Contents
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.
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 ...
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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