Lecture and Exercise Protein Prediction I for Bioinformaticians SoSe 17

 

Type:

Lecture (4 SWS) + Exercise (2 SWS)

ECTS:

8.0

Lecturer

Burkhard Rost  (lecture)
tba (exercise)

Lecture:

Tuesday, 12:30 - 14:00

  • Room: MI 01.09.034 (Rostlab seminar room)

Thursday, 12:30 - 14:00

  • Room: MI 01.09.034 (Rostlab seminar room)

Exercise:

Thursday, 14:00 - 15:30

  • Room: MI 01.09.034 (Rostlab seminar room)

Exam:

WEDNESDAY(!!) July 12. 18:30-20:00, MW 1801, engineering building, Ernst-Schmidt-Hörsaal (5508.01.801)

Make-up exam: TBC!!!!! Oct 17 & 19, 2017 - lecture time

Language:

English

Announcements:

 

  • Please be aware that some details are currently modfied. Please come back regularly

Content

Topics will include (but not be limited to):

  • Intro: what is protein function?
  • 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.

Slides:

02.05 Intro 1Video

04.05 Intro 2: StructureVideo

11.05 Alignments 1Video

16.05 Alignments 2 – Video

18.05 Comparative ModellingVideo

01.06 Secondary Structure Prediction 2Video

08.06 Secondary Structure Prediction 3Video

13.06 Transmembrane Helix PredictionVideo

20.06 TMSEG (Michael Bernhofer)Video

22.06 Beta Membrane & AccessibilityVideo

27.06 Protein DisorderVideo

06.07 Exomic Variation Effects PredictionVideo

Exercise:

May 4th

June 1st

June 8th CSV file JupyterNotebook (HTML)

June 22nd

June 29th