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

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
• Canavan Disease
• Fabry Disease
• Gaucher Disease
• Hemochromatosis
• Maple Syrup Urine Disease
• Phenylketonuria
• Tay-Sachs Disease

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
• Software
• Databases

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
• 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, 10 am. Discussion of task 3; presentation of task 4: Structural alignment
• May 21. No meeting! Whitsun holiday (Pfingsten)
• May 28, 10 am. Discussion of task 4; presentation of task 5: Homology modelling
• June 4, 10 am. Discussion of task 5; presentation of task6: Protein structure prediction from evolutionary sequence variation
• June 11, 10 am. Discussion of task 6; presentation of task 7: Researching SNPs
• June 18, 10 am. Discussion of task 7; presentation of task 8: Sequence-based mutation analysis
• June 25, 10 am. Discussion of task 8; presentation of task 9: Structure-based mutation analysis
• July 2, 10 am. Discussion of task 9; presentation of task 10: Normal Mode Analysis
• July 9, 10 am. Discussion of task 10; presentation of task 11: Molecular dynamics
• July 16, 10 am. Discussion of task 11