Difference between revisions of "Protein Structure and Function Analysis (version: SS 2011)"

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== Tasks ==
 
== Tasks ==
   
# [[task_diseaseInfo|Collect information on the individual disease]]
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# [[task_diseaseInfo|Collect information on the individual disease]] -- put into wiki by: '''May 17th'''
# [[task_alignments|Sequence alignments (sequence searches and multiple alignments)]]
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# [[task_alignments|Sequence alignments (sequence searches and multiple alignments)]] -- get results by: '''May 24th'''; see '''update''' on the HHsearch task!
# [[task_sequenceAnalysis|Sequence based analyses (Conservation, secondary structure, etc.)]]
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# [[Task_3_-_Sequence-based_predictions|Sequence-based analyses]]
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# [[task_homologyModelling|Homology based structure predictions]] -- '''see [[Resource software|Software]] section''' for hints how to get Modeller to work (thanks Markus!)
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# [[Task_5_-_Mapping_SNPs| Mapping point mutations]]
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# [[Task_6_-_Sequence-based_mutation_analysis| Sequence-based mutation analysis]]
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# [[Task_7_-_Structure-based_mutation_analysis| Structure-based mutation analysis]]
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# [[Task_8_-_Molecular_Dynamics_Simulations| Molecular Dynamics Simulations]]
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# [[Task_9_-_Normal_Mode_Analysis|Normal mode analysis]] -- '''see [[Animated Gifs|Animated Gifs]] section''' for hints how to get an animated gif for the wiki
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# [[Task_10_-_Molecular_Dynamics_Simulations| Molecular Dynamics Simulations Analysis]]
   
 
== Diseases ==
 
== Diseases ==
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* [[Example/Template]]
 
* [[Example/Template]]
   
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* [[Phenylketonuria]]
 
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* [[Gaucher Disease]]
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* [[Hemochromatosis]]
   
 
* [[Maple syrup urine disease]]
 
* [[Maple syrup urine disease]]
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* [[Metachromatic leukodystrophy]]
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* [[Phenylketonuria]]
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* [[Tay-Sachs Disease]]
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* [[Werner Syndrome]]
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* [[Fabry Disease]]
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* [[Canavan Disease]]
   
 
== Resources ==
 
== Resources ==
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== Important Dates ==
 
== Important Dates ==
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This is the current schedule for the tasks we will discuss. As the practical progresses we might need to shift dates in order to give time to address some problems in more detail.
* First meeting: May 10th, 10 am; students present their assigned diseases (see Task 1)
 
* Second meeting: May 17th, 10 am; introduction to "Sequence alignments" (see Task 2)
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* Meeting: '''May 10th''', 10 am; students present their assigned diseases (see [[task_diseaseInfo|Task 1]])
* Third meeting: May 24th, 10 am; discussion of "Sequence alignment" task results, problems etc AND introduction to "Sequence based analysis" (see Task 3)
+
* Meeting: '''May 17th''', 10 am; introduction to "Sequence alignments" (see [[task_alignments|Task 2]])
  +
* Meeting: '''May 24th''', 10 am; discussion of "Sequence alignment" task results, problems etc AND introduction to "Sequence based analysis" (see [[Task_3_-_Sequence-based_predictions|Task 3]])
  +
* '''no meeting''' on May 31st due to [http://mpi.fs.tum.de/events/studentische-vollversammlung-am-31.-mai-2011 "Studentische Vollversammlunng"]
  +
* Meeting: '''June 7th''', 10 am; discussion of "Sequence based analysis" task results AND introduction to "Homology modelling" (see [[task_homologyModelling|Task 4]])
  +
* '''no meeting''' on June 14th due to the Whit holiday
  +
* Meeting: '''June 21st''', 10 am; discussion of "Homology modelling" task results AND introduction to "Databases: HGMD etc" and discussion of the results (see [[Task_5_-_Mapping_SNPs|Task 5]]) AND introduction to "Sequence based mutation analysis"
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* Meeting: '''June 28th''', 10 am; discussion of "Sequence based mutation analysis" task results AND introduction to "Structure based mutation analysis"
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* Meeting: '''July 5th''' , 10 am; discussion of "Structure based mutation analysis" task results AND introduction to "Molecular dynamics"
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* Meeting: '''July 12th''' , 10 am; first discussion of "Molecular dynamics" task results AND introduction to "Normal mode analysis"
  +
* Meeting: '''July 20th''', ''''' 9 am'''''; '''CANCELED'''
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* Meeting: '''July 26th''' , 10 am; discussion of "Normal mode analysis" AND "Molecular dynamics" task results
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* depending on progress - potential meeting on '''August 4th''', 10 am; wrap up

Latest revision as of 15:12, 20 February 2012

This is the main information exchange for the practical on Protein Structure and Function Analysis in 2011. 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 -- put into wiki by: May 17th
  2. Sequence alignments (sequence searches and multiple alignments) -- get results by: May 24th; see update on the HHsearch task!
  3. Sequence-based analyses
  4. Homology based structure predictions -- see Software section for hints how to get Modeller to work (thanks Markus!)
  5. Mapping point mutations
  6. Sequence-based mutation analysis
  7. Structure-based mutation analysis
  8. Molecular Dynamics Simulations
  9. Normal mode analysis -- see Animated Gifs section for hints how to get an animated gif for the wiki
  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. Form 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 in order to give time to address some problems in more detail.

  • Meeting: May 10th, 10 am; students present their assigned diseases (see Task 1)
  • Meeting: May 17th, 10 am; introduction to "Sequence alignments" (see Task 2)
  • Meeting: May 24th, 10 am; discussion of "Sequence alignment" task results, problems etc AND introduction to "Sequence based analysis" (see Task 3)
  • no meeting on May 31st due to "Studentische Vollversammlunng"
  • Meeting: June 7th, 10 am; discussion of "Sequence based analysis" task results AND introduction to "Homology modelling" (see Task 4)
  • no meeting on June 14th due to the Whit holiday
  • Meeting: June 21st, 10 am; discussion of "Homology modelling" task results AND introduction to "Databases: HGMD etc" and discussion of the results (see Task 5) AND introduction to "Sequence based mutation analysis"
  • Meeting: June 28th, 10 am; discussion of "Sequence based mutation analysis" task results AND introduction to "Structure based mutation analysis"
  • Meeting: July 5th , 10 am; discussion of "Structure based mutation analysis" task results AND introduction to "Molecular dynamics"
  • Meeting: July 12th , 10 am; first discussion of "Molecular dynamics" task results AND introduction to "Normal mode analysis"
  • Meeting: July 20th, 9 am; CANCELED
  • Meeting: July 26th , 10 am; discussion of "Normal mode analysis" AND "Molecular dynamics" task results
  • depending on progress - potential meeting on August 4th, 10 am; wrap up