More exercises?

Some of you have asked for more exercises lest they forget what they have learnt in the workshop.

I will add some links below, but remember: Google is your friend!

http://www.macalester.edu/~shoop/courses/CHEM58_S03/index.html

Combat bacteria using computational biology

Using computational biology, you may be able to predict antibiotic effectiveness and resistance

PDB educational features and new tools

The Protein Data Bank (PDB) is currently evolving. The new beta site is out and is expected to be released soon in a stable version.

Also, there are two interesting features that need to be highlighted in PDB:

– Educational resources, especially the “Molecule of the month” feature

– For any given molecule, try to view the structures in “Protein Workshop” format. This format does not require you to download/install any software. Once you click on the link, an java-based application will open. This should work on most new systems (i.e., not older than 3-4 computers)

From Science: A Scientist’s Nightmare: Software Problem Leads to Five Retractions

Science 22 December 2006

Vol. 314. no. 5807, pp. 1856 – 1857
DOI: 10.1126/science.314.5807.1856

News of the Week

SCIENTIFIC PUBLISHING:
A Scientist‘s Nightmare: Software Problem Leads to Five Retractions

Greg Miller Until recently, Geoffrey Chang’s career was on a trajectory most young scientists only dream about. In 1999, at the age of 28, the protein crystallographer landed a faculty position at the prestigious Scripps Research Institute in San Diego, California. The next year, in a ceremony at the White House, Chang received a Presidential Early Career Award for Scientists and Engineers, the country’s highest honor for young researchers. His lab generated a stream of high-profile papers detailing the molecular structures of important proteins embedded in cell membranes.

read on

Bioinformatics and the epidemiology of Influenza A

A very recent and very powerful study was recently published in the open-access journal: PLOS Pathogens, one of the top journals on Microbiology and Infectious disesases…

Stochastic Processes Are Key Determinants of Short-Term Evolution in Influenza A Virus

The article is not very easy and is full of terms that need background knowledge, but you should get a good idea on the work from the Abstract (Synopsis) and Introduction.

Bioinformatics for vaccine development

Most of you asked for more/better examples that show how bioinformatics alone can lead to discovery and practical applications.
Here is one paper  I  found: In silico and microarray-based genomic approaches to identifying potential vaccine candidates against Leptospira interrogans.

Course evaluation

Please remember to turn in the course evaluation forms (filled).

Literature Mining Tools

We have discussed today two different literature-mining tools.

1) PubMed Reminer: Detailed analysis of PubMed search results.

PubReMiner will query pubmed with your specified searchquery, get all abstracts and generate frequency tables.
The first table will show you journals in which your query is published the most.
The second table will show you the authors which are most active in the field of your query.
The third table will show you words that have been used most in the title and abstract of the articles.
furthermore, Addressfields, MESH headers and publication year are displayed.
All elements can be added to your query, and will thus make sure that your refinement still generates results.
When you are satisfied with the query, you can jump to pubmed and view the results.
Alternative names: PubReMiner, pubmed reminer, pub reminer, pubmed re-miner

2) Chilibot! The smart literature miner…

Find relationships from PubMed abstracts…

Tutorial 4: Peptide fingerprinting questions

A- Use Aldente or MS-Fit to identify the following proteins.

1. A protein that was identified on a 2D-gel with an approximate MW of 35 kDa and an isoelectric point of 8.4.
   After trypsin digestion and MS analysis, the following masses were obtained:

   1261.59
   1211.4
   1111.64
   963.48
   950.49
   871.54
   842.54
   751.5
   721.354
   609.33

2. During a co-immunoprecipitation experiment (what is it?), a protein with a MW around 50 kDa and pI about 5, was identified to bind to HSP 60.
   The peptide fingerprinting results were as follow:

   1272.24
   702.352
   645.36
   1076.5
   1115.7
   861.32
   1169.7
   1323.6
   1471.2
   1405.7
   1588.644

   There was a closely related form of the protein with the following, slightly different peptide masses:

   872.41
   702.352
   645.36
   1076.5
   1115.7
   701.39
   1169.7
   1323.6
   1471.2
   1405.7
   1428.7117

   Identify the protein and explain the slight differences in MS results.

3. Have you noticed differences between Aldente and MS-FIT? Discuss the differences…
4. How does the choice of search database affect peptide fingerprinting results?

Tutorial 3/2: ClustalW

1) Retrieve the sequence of the following proteins from Streptococcus pyogenes: SpeA (Streptococcal pyrogenic exotoxin A), SpeC, SpeG, SpeJ, and SmeZ (Streptococcal mitogenic exotoxin Z). All these proteins are streptococcal toxins with superantigenic properties.

2) Put all sequences in FASTA format (in a Word file). Modify the FASTA identifier line (i.e., the line starting with >) so that it only contains the protein symbol (This will make the following steps easier).

3) Use either NPS@ or EBI ClustalW (Both sites are linked in the side bar under “Blogroll”) to align all the five toxins.

4) Discuss with your colleague whether you can guess the active site of these superantigenic toxins from the multiple sequence alignment. To verify your answer or support your claim, search Pubmed and find whether anybody has worked on conserved residues in superantigens.