Protein Prediction II for Computer Scientists WS14/15


Lecture (4 SWS) + Exercise (2 SWS)




Burkhard Rost  (lecture)
Tatyana Goldberg (exercise)
Juan Miguel Cejuela (exercise)


Tuesday, 11:00 - 12:30 (lecture)
Thursday, 11:00 - 12:30 (lecture)
Thursday, 12:30 - 13:30 (exercise)


Lecture: FMI 01.09.034

Exercise: FMI 00.04.011

Exam: January 22, 2015, 17:30-19:00, Interims Hörsaal 2




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No lecture on Tuesday Nov. 4 due to Student Assembly.

The first exercise takes place on Thursday Oct. 16.  The exercise on Oct. 16 will take place in the RostLab seminar room FMI 01.09.034.

No lectures on Tuesday Oct. 14 and Thursday Oct. 16 due to illness.

Lecture starts on Oct. 9 and the exercise on Oct. 16

Examen: January 22, 2015 (Important: Don't forget to register at TUMonline for the exam)

  • Makeup: tba


This lecture continues the 'Protein Prediction I' lecture. The attendance of this lecture however is not a mandatory requirement for 'Protein Prediction II'. Topics will include (but not be limited to):

  • Predicting protein function using sequence: sequence alignments, multiple sequence alignments, motifs, domain assignment, annotation transfer by homology, ab initio predictions.
  • Predicting protein function using structure: structural alignments, structural motifs, annotation transfer via structure similarity.
  • From structure prediction to function prediction: comparative modeling; prediction of: secondary structure, hydrophilicity profiles, solvent accessibility, transmembrane segments, disordered regions, contact maps, functional residues; template free modeling.
  • Machine learning.


20141021: Personalized health - Burkhard Rost -  Slides Video (1080p)

20141023: Introduction to protein function - Burkhard Rost - Slides Video (1080p)

20141028: Homology-based prediction of protein function 1 - Tobias Hamp - Slides Video (1080p)

20141030: Homology-based prediction of protein function 2 - Tobias Hamp - Slides Video (1080p)

20141106/20141111: Homology-based prediction of protein function 3 - Burkhard Rost - Slides No video (last year's) / Video (1080p)

20141113: Chalk talk, no video

20141118: Prediction of sub-cellular localization 1 - Burkhard Rost - Slides

20141120: Prediction of sub-cellular localization 2 - Tatyana Goldberg - Slides Video (1080p)

20141125: Prediction of sub-cellular localization 1 - Burkhard Rost - Slides Video (1080p)

20141127: Prediction of sub-cellular localization 3 - Burkhard Rost - Slides cont'd from 25.11. Video (1080p)

20141202: Predict protein-protein interaction sites - Burkhard Rost - Slides Video (1080p)

20141209: Sequence motifs: Representing, matching and discovering -  Mikael Bodén - Slides Video (1080p)

20141211: Sequence motifs 2 -  Mikael Bodén - Slides cont'd from 9.12. Video (1080p)

20141216: 3D function prediction -  Andrea Schafferhans - Slides Video (1080p)

20141218: Protein-ligand interactions docking -  Andrea Schafferhans - Slides Video (1080p)

20150113: Predicting protein interaction pairs -  Burkhard Rost - Slides Video (1080p)


The advances of high-throughput sequencing technologies have resulted in an ever growing amount of biological data. Visualization is in an intuitive way to analyze these data. In the exercises we will be working on the development of novel JavaScript-based components to visualizate biological data on the web.

For more details please refer to our wiki. The organisation, requirements and grading of the exercise are also explained there.The log in credentials will be announced in the exercise on Oct 16th.