Lecture 'Protein Prediction' SS 2012

  

Type:

Lecture (4 SWS) + Exercise (2 SWS)

Ects:

8.0

Lecturer

Burkhard Rost  (lecture)
Tobias Hamp, Esmeralda Vicedo (exercise)

Rotation:

Tuesday, 13:00 - 14:30 (lecture)
Thursday, 10:00 - 11:30 (lecture)
Thursday, 11:30 - 13:00 (exercise)

Rooms:

Lecture:
Tuesdays: MW1250 (Building 'Maschinenwesen' (MW), Boltzmannstr. 15)
Thursdays: MI 00.08.038 (Small Multimedia Room, Boltzmannstr. 3)
Exercise: MI 00.08.038 (Small Multimedia Room, Boltzmannstr. 3)

 

Language:

English

 

 

Announcements:

Lecture series starts on Thursday, April 19 ; No lecture on Thursday June 14, the exercises will take place at the usual time.
 

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 - 20120424 - PP1 - Burkhard Rost - "Introduction PP1 Summer 2012 - Intro1: amino acids"

Lecture 2 - 20120426 - PP1 - Burkhard Rost - "Introduction PP1 Summer 2012 - Machine Learning For Molecular Biology"

Lecture 3 - 20120503 - PP1 - Burkhard Rost - "Introduction PP1 Summer 2012 - Membrane Prediction 1"

Lecture 4 - 20120508 - PP1 - Andrea Schafferhans - "Introduction PP1 Summer 2012 - Structure Comparison"

Lecture 5 - 20120510 - PP1 - Andrea Schafferhans - "Introduction PP1 Summer 2012 - Structure Prediction Part I"

Lecture 6 - 20120522 - PP1 - Andrea Schafferhans - "Introduction PP1 Summer 2012 - Structure Prediction Part II"

Lecture 7 - 20120524 - PP1 - Burkhard Rost - "Alignments - Alignments 1"

Lecture 8 - 20120531 - PP1 - Burkhard Rost - "Alignments - Alignments 2"

Lecture 9 - 20120605 - PP1 - Burkhard Rost - "Secondary structure assignment Summer 2012 - secstr_assign"

Lecture 10 - 20120612 - PP1 - Burkhard Rost - "Secondary Structure Prediction 1 Summer 2012- SecStrPred_1 (White Board)"

Lecture 11 - 20120619 - PP1 - Burkhard Rost - "Secondary Structure Prediction 1 Summer 2012- SecStrPred_1"

Lecture 12 - 20120621 - PP1 - Burkhard Rost - "Secondary Structure Prediction 2 Summer 2012- SecStrPred_2"

Lecture 13 - 20120626 - PP1 - Thomas Hopf - "Membrane protein 3D prediction "

Lecture 14 - 20120628 - PP1 - Burkhard Rost - "Transmembrane strands & accessibility & 2D prediction Summer 2012 - TMB_acc"

 

Exercise: