RPR-SX-PDB

Analyzing PDB files

 

Keywords:  Practical work with the PDB, the R bio3d package

 

 

 

Abstract

PDB structures are complex objects to which we can apply a number of measures - but doing so requires that we can read and analyze them in the computer. In this unit we explore computational analysis of PDB structures using bio3D.

 

This unit ...

Prerequisites

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

• BIN-PDB (The RCSB-PDB Structure Database)

 

Objectives

This unit will ...

• ... introduce the bio3d package;
• ... demonstrate quantitative analysis of PDB files;
• ... teach plotting techniques for density plots;
• ... explore database-scale work with PDB files.

 

Outcomes

After working through this unit you ...

• ... are familar with PDB objects in the bio3d package;
• ... can investigate features of PDB structures both in individual structures and collections of structures, and plot and interpret the results.

 

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

This learning unit can be evaluated for a maximum of 6 marks. If you want to submit tasks for this unit for credit you have the following options. If you have any questions about these options, discuss on the mailing list.

Short Report option

1. Create a new page on the student Wiki as a subpage of your User Page.

2. Select a unique set of fifteen representative PDB structures by issuing the command:

(myPDBs <- selectPDBrep(15))

3. Analyze the distribution of H-bonds in helices and strands of your fifteen structures. Interpret your findings: what is the source of the difference, what seems to be the lowest energy distance between N...O in a Hydrogen bond?

4. Count the number of cis-peptide bonds in your structures. Do this separately for prolines, and for all other residues. Do you find that X-Pro cis-peptide bonds are more frequent than others? Why is that?

5. Plot chi1 torsion angles of amino acid sidechains againt chi2 torsion angles to analyze sidechain rotamer distributions. Aim for a publication quality plot and include the plot and its caption in your report. Choose one of the following amino acids for your analysis:

tyrosine, phenylalanine, histidine, tryptophan, isoleucine, leucine, asparagine or aspartic acid. Interpret the results.

6. Form matters. Be neat, and concise! Be sure to include a list of your PDB IDs in your report! Make sure your process is documented, your results are presented, and that everything is interpreted. At the end of your report, include a section that contains all of the R script(s) you have written for your analysis. Make sure that your scripts are clean, error-free and commented. Also make absolutely sure that you have referenced all contributions that are not originally your own.

7. When you are done with your report, add the following category tag to the page:

[[Category:Eval-RPR-SX-PDB]]

Do not change your submission page after this tag has been added. The page will be marked and the category tag will be removed by the instructor.

 

 

Contents

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-SX-PDB.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.

 

 

 

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:

2017-10-17

Version:

1.0

Version history:

• 1.0 First live version
• 0.1 First stub

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