Lecture 'Protein Prediction' SS 2013

News:
The grades are published in TUMonline now. The exam inspection will take place on Thursday, September 26, 10-12am, room MI 01.09.034.

Type:

Lecture (4 SWS) + Exercise (2 SWS)

Ects:

8.0

Lecturer

Burkhard Rost  (lecture)
Tatyana Goldberg, Maximilian Hecht, Lothar Richter, Christian Schaefer (exercise)

Lecture:

Tuesday, 12:30 - 13:30 (Computational Biology students)

  • Room: 01.09.034 (MI, Boltzmannstr. 3; 1.OG)

Tuesday, 13:45 - 14:45 (Informatics students)

  • Room: MW 1250 (Maschinenwesen; Boltzmannstr. 15; 1. OG)

Thursday, 10:00 - 11:00 (Informatics students)

  • Room: MI 00.06.011 (Hörsaal 3)

Thursday, 11:15 - 12:15 (Computational Biology students)

  • Room: 01.09.034 (MI, Boltzmannstr. 3; 1.OG)

Exercise:

Thursday, 12:30 - 13:30

  • Groups 1-8 & 25-28: MI 01.09.034 (Our Seminar Room)
  • Groups 9-16 & 17-24: MI 00.08.038 (Small Multimedia Room)

Each group will meet the tutors every two weeks.

Exam:

July 9, 12:00 - 13:30, HS 1 (Lecture Hall 1) 00.02.001

  • Makeup: October 17, 10:00 - 12:00

!! Makeup exam registration via TUMOnline, September 2nd - 16th !!

The participants have been informed about the time schedule by email to their TUMonline account.

It will be held as oral exam, room number 01.09.054.

 

Language:

English

Announcements:

  • Lecture series start on Tuesday, April 16. Exercises start on Thursday, April 18. (Participation in the first exercise is mandatory!).
  • No lecture on Thursday, May 9; Tuesday, May 14; Thursday, May 30
  • Tutors are available for project-related questions on Thursdays 10:00 - 12:15.
  • Unfortunately student machines are currently down. We are trying to solve the problem ASAP.
  • The student computers are up and accessible over SSH. The machine names range from i12k-biolab01-i12k-biolab10 and i12k-biolab12-i12k-biolab14
  • No lecture on Thursday, May 2nd, however, there is an exercise.
  • Please do NOT install software on student machines. If there is a program missing, let the tutors know.
  • Group lists updated on May 8.
  • No new student registrations and group re-arrangements are possible!
  • !! The web site for Predict Protein testing is http://pp-dev.informatik.tu-muenchen.de:8080/ !!
  • There will be no points for testing any other URL
  • Testing recipes can be found here
  • The exam inspection will take place on Thursday, September 26, 10-12am, room MI 01.09.034.  

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.

Materials

Lecture:

Lecture 1 - 20130423 - PP1 - Burkhard Rost - "Introduction - Life, molecules, parts"

Lecture 2 - 20130425 - PP1 - Burkhard Rost - "Machine learning in biology"

Lecture 3 - 20130430 - PP1 - Burkhard Rost - "Protein structure"

Lecture 4 - 20130507 - PP1 - Burkhard Rost - "Alignments 1"

Lecture 5 - 20130523 - PP1 - Burkhard Rost - "Alignments 2"

Lecture 6 - 20130528 - PP1 - Burkhard Rost - "Alignments 3"

Lecture 7 - 20130604 - PP1 - Burkhard Rost - "Comparative Modeling 1"

Lecture 8 - 20130606 - PP1 - Burkhard Rost - "Comparative Modeling 2"

Lecture 9 - 20130611 - PP1 - Burkhard Rost - "Structure determination"

Lecture 10 - 20130613 - PP1 - Burkhard Rost - "Secondary Structure prediction"

Lecture 11 - 20130618 - PP1 - Burkhard Rost - "Secondary Structure prediction 2"

Lecture 12 - 20130620 - PP1 - Burkhard Rost - "Membrane helix prediction"

Lecture 13 - 20130625 - PP1 - Burkhard Rost - "Beta membrane, accessibility & 2D"

Exercise: