Difference between revisions of "Protein Structure and Function Analysis (SS 2013)"

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This is the main information exchange for the [http://rostlab.org/cms/teaching/teaching-overview/pracstrucfunc13/ practical on Protein Structure and Function Analysis in 2013].
  
This is the main information exchange for the [http://rostlab.org/cms/teaching/teaching-overview/pracstrucfunc13/ 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.
  
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.
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== Tasks ==
  
== Tasks ==
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# [[Task_alignments|Run sequence searches on the disease gene product and produce alignments]]
  
# [[Task_alignments|Run sequence searches on the disease gene product and produce alignments]]
 
# [[Task_3_-_Sequence-based_predictions|Prediction of different features from protein sequence]]
  
# [[Task_3_-_Sequence-based_predictions|Prediction of different features from protein sequence]]
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# [[Task_strucAli|Structural alignment, evaluation of alignments using structures]]
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# [[Task_Structural_Alignments|Structural alignment, evaluation of alignments using structures]]
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# [[Task_Homology_Modelling|Homology based structure prediction]]
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#
  
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# [[Task_6_-_Protein_structure_prediction_from_evolutionary_sequence_variation|Protein structure prediction from evolutionary sequence variation]]
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#
  
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# [[Task_7_Research_SNPs|Researching SNPs]]
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#
  
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# [[Task_8_Sequence-based_mutation_analysis|Sequence-based mutation analysis]]
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# [[Task_9_Structure-based_mutation_analysis|Structure-based mutation analysis]]
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# [[Task_10_-_Normal_Mode_Analysis|Normal mode analysis]]
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# [[Task_11_-_Molecular_Dynamics_Simulation|Molecular dynamics simluation]]
   
 
== Diseases ==
  
== 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.
  
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.
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* [[Example/Template]]
  
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[[Example/Template]]
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* [[Canavan Disease]]
  
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* [[Gaucher Disease]]
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# [[Canavan Disease]]
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* [[Hemochromatosis]]
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# [[Gaucher Disease]]
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# [[Hemochromatosis]]
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* [[Maple Syrup Urine Disease]]
  
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# [[Maple Syrup Urine Disease]]
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* [[Phenylketonuria]]
  
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# [[Phenylketonuria]]
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== Resources ==
  
== Resources ==
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* [[resource_language|Language]]
  
* [[resource_language|Language]]
 
* [[resource_discussion|Discussion]]
  
* [[resource_discussion|Discussion]]
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== Important Dates ==
  
== Important Dates ==
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* '''June 25''', 10 am. Discussion of task 7; presentation of task 8: Sequence-based mutation analysis
  
* '''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 2''', 10 am. Discussion of task 8; presentation of task 9: Structure-based mutation analysis
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* '''July 9''', 10 am. Discussion of task 9; presentation of task 10: Normal Mode Analysis
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* '''July 9''', 10 am. '''''No meeting!''''' Exam. Discussion and talk shifted to July 16
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* '''July 16''', 10 am. Discussion of task 10; presentation of task 11: Molecular dynamics
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* '''July 16''', 12 am. '''''Meeting is shifted to 12 pm, end approx. 2:30 pm.''''' Discussion of task 9; presentation of task 10: Normal Mode Analysis; presentation of task 11: Molecular dynamics
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* end of July ?, ? am. Discussion of task 11
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* '''July 30''', 10 am. Discussion of task 10; discussion of task 11 and all other tasks optional
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* '''Wednesday, August 14''', 11 am. Final discussion of the practical
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'''Deadlines'''
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* '''August 31:''' Finalize wiki
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* '''September 30: ''' Hand in report
   
 
== What to put on the Wiki ==
  
== What to put on the Wiki ==
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* Discuss the outcome: Try to make sense of what you observed. Would you have expected that outcome? Why / why not?
  
* 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.
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* We recommend separating the "lab journal" part from the Results and Discussion part.
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* Remember: spellcheck; reference your figures in the text; font size in figures should be large enough to be readable; paragraphs min. 3 sentences, but not too long; sentences not too long.
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* '''Deadline:''' August 31
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  +
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== Talks ==
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Your first task is giving a short talk presenting your disease: [[task_diseaseInfo|Collect information on the individual disease]]. During the practical, each student will give a methodological talk, introducing one of the tasks (15-20 min, see respective [https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Protein_Structure_and_Function_Analysis_%28SS_2013%29#Tasks task] for more information).
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== Report ==
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Write a report of your findings during the practical. Guidelines:
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* max. 5 pages
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* Bioinformatics style. Templates of the journal can be found here for [http://www.oxfordjournals.org/our_journals/bioinformatics/for_authors/submission_online.html LaTeX] and [http://www.oxfordjournals.org/our_journals/bioinformatics/for_authors/submission_online.html Word].
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* Scientific report, i.e. should not contain ALL your results, but (based on your results) present an interesting story.
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* Remember: spellcheck; reference your sources; reference your figures in the text; font size in figures should be large enough to be readable; paragraphs min. 3 sentences, but not too long; sentences not too long.
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* '''Deadline:''' September 30

Latest revision as of 19:29, 23 April 2014

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
  8. Sequence-based mutation analysis
  9. Structure-based mutation analysis
  10. Normal mode analysis
  11. Molecular dynamics simluation

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


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. No meeting! Exam. Discussion and talk shifted to July 16
  • July 16, 12 am. Meeting is shifted to 12 pm, end approx. 2:30 pm. Discussion of task 9; presentation of task 10: Normal Mode Analysis; presentation of task 11: Molecular dynamics
  • July 30, 10 am. Discussion of task 10; discussion of task 11 and all other tasks optional
  • Wednesday, August 14, 11 am. Final discussion of the practical


Deadlines

  • August 31: Finalize wiki
  • September 30: Hand in report

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 separating the "lab journal" part from the Results and Discussion part.
  • Remember: spellcheck; reference your figures in the text; font size in figures should be large enough to be readable; paragraphs min. 3 sentences, but not too long; sentences not too long.
  • Deadline: August 31


Talks

Your first task is giving a short talk presenting your disease: Collect information on the individual disease. During the practical, each student will give a methodological talk, introducing one of the tasks (15-20 min, see respective task for more information).


Report

Write a report of your findings during the practical. Guidelines:

  • max. 5 pages
  • Bioinformatics style. Templates of the journal can be found here for LaTeX and Word.
  • Scientific report, i.e. should not contain ALL your results, but (based on your results) present an interesting story.
  • Remember: spellcheck; reference your sources; reference your figures in the text; font size in figures should be large enough to be readable; paragraphs min. 3 sentences, but not too long; sentences not too long.
  • Deadline: September 30
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