Lecture 'Protein Prediction II' WS 2012/2013

Type:

Lecture (4 SWS) + Exercise (2 SWS)

Ects:

8.0

Lecturer

Burkhard Rost  (lecture)
Tatyana Goldberg, Maximilian Hecht (exercise)

Rotation:

Tuesday, 13:15 - 14:45 (lecture)
Thursday, 11:00 - 12:30 (lecture)
Thursday, 12:30 - 13:15 (exercise)

Place:

Lecture: Tuesday: MI 01.09.034 , Thursday: MI 01.09.034 
Exercise: MI 01.09.034

Language:

English

 

Announcements:

No Lecture/Exercise on Thursday, Dec 6th

The videos can be downloaded on this page

Examen: Feb 07, 11:00, MI 00.08.038 (Important: Don't forget to register at TUMonline for the exam)

  • Makeup: March 04, 2013

Content

This lecture continues the 'Protein Prediction' lecture. 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.

Materials

 
Lecture:

Lecture 1 - 20121018 - PP2 - Burkhard Rost - "Welcome: who we are"

Lecture 2 - 20121023 - PP2 - Burkhard Rost - "Individualized health"

Lecture 3 - 20121025 - PP2 - Burkhard Rost - "Introduction to protein function 1"

Lecture 4 - 20121030 - PP2 - Tatyana Goldberg - "Predict localization"

Lecture 5 - 20121106 - PP2 - Burkhard Rost - "Introduction to protein function 2"

Lecture 6 - 20121108 - PP2 - Burkhard Rost - "Introduction to protein function 3"

Lecture 7 - 20121113 - PP2 - Burkhard Rost - "Predict localization 2"

Lecture 8 - 20121115 - PP2 - Tobias Hamp - "Homology-based prediction of function"

Lecture 9 - 20121120 - PP2 - Burkhard Rost - "Predict localization 3"

Lecture 10 - 20121122 - PP2 - Burkhard Rost - "Predict localization 4"

Lecture 11 - 20121204 - PP2 - Burkhard Rost - "SNP effect 1"

Lecture 12 - 20121211 - PP2 - Burkhard Rost - "SNP effect 2"

Lecture 13 - 20121218 - PP2 - Andrea Schafferhans - "Enzymes"

Lecture 14 - 20130108 - PP2 - Burkhard Rost -"Predict protein interactions 1"

Lecture 15 - 20130110 - PP2 - Burkhard Rost -"Predict protein interactions 2"

Lecture 16 - 20130115 - PP2 - Andrea Schafferhans -"Docking 1"

Lecture 17 - 20130117 - PP2 - Burkhard Rost -"Predict DNA/RNA binding"

Lecture 18 - 20130122 - PP2 - Andrea Schafferhans -"Docking 2"

Lecture 19 - 20130129 - PP2 - Marco Punta -"The Pfam protein families database"

Lecture 20 - 20130131 - PP2 - Marco De Vivo -"Paths to drug discovery and the role of computational chemistry"

Complete lecture

 

Videos are also available on SciVee: www.scivee.tv/user/rostlab

Exercise: