Protein Structure and Function Analysis (version: SS 2012)

From Bioinformatikpedia

This is the main information exchange for the practical on Protein Structure and Function Analysis in 2012. The organisers (Marc, Edda, Andrea) 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. Sequence alignments (sequence searches and multiple alignments)
  3. Sequence-based analyses
  4. Homology based structure predictions
  5. Researching and mapping point mutations
  6. Sequence-based mutation analysis
  7. Structure-based mutation analysis
  8. Molecular Dynamics Simulations
  9. Normal mode analysis
  10. Molecular Dynamics Simulations Analysis

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.

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

Important Dates

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

  • April 17, 10 am. Task 1: presentation of diseases; homework: fill Wiki, go through T-Coffee tutorial
  • April 24, 10 am. Introduction to task 2: (multiple) sequence alignment
  • May 1, no meeting, holiday
  • May 8, 10 am. Discussion of task 2; introduction to task 3: sequence-based predictions
  • May 15, no meeting, Student reunion
  • May 22, 10 am. Discussion of task 3; introduction to task 4: homology-based predictions
  • May 29, no meeting, Whit holdidays
  • June 5, 10 am. Discussion of task 4; introduction to task 5: SNPs
  • June 12, 10 am. Discussion of task 5; introduction to task 6 sequence-based mutation analysis
  • June 19, 10 am. Discussion of task 6; introduction to task 7: structure-based mutation analysis
  • June 26, 10 am. Discussion of task 7; introduction to task 8: molecular dynamics simulation
  • July 3, 10 am. Discussion of task 8; introduction to task 9: normal mode analysis
  • July 10, 10 am. Introduction to task 10 (8b): analysis of MD; Note: discussion of task 9 -> next week
  • July17, 10 am. Discussion of task 9 and task 10 (8b)
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