Protein Structure and Function Analysis (SS 2013)

This is the main information exchange for the practical on Protein Structure and Function Analysis in 2013. The organisers (Edda, Andrea, Lothar) publish short introductions into the tasks, which are roughly organised by days of the practical. Students add their talks and use this site to document their methods and results. - You can log in to edit with the credentials for the Rostlab/Kramer student computer cluster.

Tasks

1. Collect information on the individual disease
2. Run sequence searches on the disease gene product and produce alignments
3. Prediction of different features from protein sequence
4. Structural alignment, evaluation of alignments using structures
5. Homology based structure prediction
6. Protein structure prediction from evolutionary sequence variation
7. Researching SNPs

Diseases

In this practical, we analyse the mutations causing a number of genetic diseases (see disease list). For each disease, one page summarises the information on the genetic disease. From there, we link to pages detailing the analysis results for the individual mutated sequences.

Example/Template

1. Canavan Disease
2. Gaucher Disease
3. Hemochromatosis
4. Maple Syrup Urine Disease
5. Phenylketonuria

Resources

Here, we collect links to resources used throughout the practical. This list is maintained by the organisers and the students. Please also include a short description of the resource if you add something. (Also, feel free to add to the existing descriptions.) The resources can be related to

• Literature
• Wiki editing
• Software
• Databases
• Language
• Discussion

Important Dates

This is the current schedule for the tasks we will discuss. As the practical progresses we might need to shift dates.

• April 23, 10 am. Task 1: presentation of diseases; homework: fill Wiki; (Hint: familiarise yourself with the infrastructure, look at tutorials: PSI-Blast tutorial, HHblits (tutorial=section 3) T-Coffee)
• April 30, 10 am. Discussion of diseases; presentation of task 2: Sequence alignments
• May 7, 10 am. Discussion of task 2; presentation of task 3: Sequence-based predictions
• May 14, No meeting! Studentische Vollversammlung
• May 21. No meeting! Whitsun holiday (Pfingsten)
• May 28, 10 am. Discussion of task 3; presentation of task 4: Structural alignment, evaluation of alignments using structures

• June 4, 10 am. Discussion of task 4; presentation of task 5: Homology modelling
• June 11, 10 am. Discussion of task 5; presentation of task6: Protein structure prediction from evolutionary sequence variation
• June 18, 10 am. Discussion of task 6; presentation of task 7: Researching SNPs
• June 25, 10 am. Discussion of task 7; presentation of task 8: Sequence-based mutation analysis
• July 2, 10 am. Discussion of task 8; presentation of task 9: Structure-based mutation analysis
• July 9, 10 am. IMPORTANT: This meeting will most probably be a short meeting starting at 11 am.Discussion of task 9
• July 16, 10 am. IMPORTANT: This meeting will most probably be shifted to 12 or 1 pm. Presentation of task 10: Normal Mode Analysis; presentation of task 11: Molecular dynamics
• end of July or August, ? am. Discussion of task 10, discussion of task 11 optional

What to put on the Wiki

The wiki entries referring to the tasks have several purposes:

• Use it as a lab journal to document what you did (make your results reproducible): e.g. collect what your command line looked like, which files your results are stored in, etc.
• Document your results: Describe what you observed.
• Discuss the outcome: Try to make sense of what you observed. Would you have expected that outcome? Why / why not?

We recommend to separate the "lab journal" part from the Results and Discussion part.