Protein Prediction II for Bioinformaticians WiSe 2015/2016

Type:

Lecture (4 SWS) + Exercise (2 SWS)

Ects:

8.0

Lecturer

Burkhard Rost  (lecture)
Tatyana Goldberg (exercise)
Jonas Reeb (exercise)

Rotation:

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

Place:

Lecture: MI 01.09.034

Exercise: MI 01.09.034

Exam: Maschinenwesen 5505.03.502 (3rd floor)

Time: 11.30 - 13.30

Exam review: 23.2. at 15.15 in Tanya's/Jonas's office

Language:

English

Announcements:

The latest news are always on top!

NEW!!!! Thursday, Oct. 22nd 2015: Due to health reasons the lecture of Prof. Rost must be cancelled. The exercise takes place.

Examen: XXXX (Important: Don't forget to register at TUMonline for the exam)

  • Makeup: tba

Content

This lecture continues the 'Protein Prediction' lecture. The attendance of this lecture is however not a mandatory requrement 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.

Materials

Oct 29th Diversity

Nov 3rd Introduction to Protein Function - Video: YouTube (1080p) , Download (360p)

Nov 3rd Predict PPIs through expression - Video: YouTube (1080p)

Nov 12th Function Prediction - Video: YouTube (1080p)

Nov 17th CAFA  (now with correct slides - thanks to D.N.) - Videos: Download (720p)

Nov 19th Enzymes - Videos: Download (480p)

Nov 24th Localization - Video: YouTube (1080p), YouTube part 2 (1080p)

Dec 8th Localization Protein-Protein Interaction

Jan 7th Protein-Protein Interaction Sites - Video: YouTube (1080p)

Jan 12th Protein-Protein Pairs - Video: Download (480p)

Jan 19th SNPs - Video: YouTube (1080p)

Exercise

Millions of single nucleotide variations are estimated to exist between people. Each one may result in no effect at all or any effect up to single-handedly leading to the development of fatal diseases. Methods have been developed that try to predict the effect at varying levels, i.e. anything from "molecular effect" to "leads to a disease".

In the first part of this exercise you will evaluate three methods' effect predictions for every possible variant in the complete human proteome. In the second part of the exercise you will focus on one tool (SNAP2) and evaluate how the predicted effect in the whole proteome differs between a set of model organism ranging from viruses over archaea to complex eukaryotes.

In parallel, we will run also another project where we will try to predict protein-protein interactions from human microarray data.

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 22, 2015.