Protein Prediction II Bioinformaticians WS13/14

Type:

Lecture (4 SWS) + Exercise (2 SWS)

Ects:

8.0

Lecturer

Burkhard Rost  (lecture)
Lothar Richter (exercise)

mail: pp2ex@rostlab.org

Rotation:

Tuesday, 12:45 - 14:15 (lecture)
Thursday, 12:45 - 14:15 (lecture)
Thursday, 14:15 - 15:15 (exercise)

Place:

Exam room: MI 01.09.014 (see Announcements below)

Lecture: Tuesday: MI 01.09.034 , Thursday: MI 01.09.034 

Exercise: MI 01.09.034

Language:

English

Announcements:

Review and Inspection is open until March 14th. Please arrange for an appointment (email to pp2ex@rostlab.org).

The final exam takes place in room 01.09.014 on Thursday, Feb 6th between 12 and 14 o'clock

No lecture/exercise on Tuesday, Feb 4th due to another exam

No lecture/exercise on Dec 12th because of Dies Academicus

No lecture on Tuesday Nov 12th because of SSV (Students' Plenum)

No lecture on Oct. 31st, but the exercise takes place

Please note: The first lecture in the winter semester 2013/14 will take place on Thursday, October 17th, in room MI 01.09.034 (Boltzmannstr. 3).

Examen: Feb 4th (Important: Don't forget to register at TUMonline for the exam)

  • Makeup: tba

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 slides Oct. 22nd Individual Health (Video)

Lecture slides Oct. 24th Introduction to Protein Function (Video)

Lecture slides Oct. 29th Homology Based Prediction of Protein Function

Lecture Slides Nov. 5th Introduction to Protein Function 2 (Video)

Lecture Slides Nov. 7th Introduction to Protein Function 3 (Video)

Lecture slides Nov. 14th Prediction of Localization 1 (Video)

Lecture slides Nov 19th Prediction of Localization 2 (Video)

Lecture slides Nov 21st Prediction of Localization 3

Lecture slides Nov 26th Protein Interaction Networks (Video)

Lecture slides Noc 28th Cont'd from Nov 21st (Video)

Lecture slides Dec. 3rd Paths to drug discovery and the role of computational chemistry (Video)

Lecture slides Dec. 5th The Pfam protein family database (Video)

Lecture slides Dec. 17th Protein ligand interactions and docking

Lecture slides Dec. 19th Protein ligand interactions and docking (Video)

 Lecture slides Jan 7th No slides, only white-board

Lecture slides Jan. 9th Protein-Protein Interaction 2 (Video)

Lecture slides Jan. 14th. Protein-Protein Interaction 2 cont'd (Video)

Lecture slides Jan. 16th Protein-Protein Interaction 3 cont'd (Video)

Lecture slides Jan 21st DNA-RNA (Video)

Lecture slides Jan 23rd SNP (Video)

Exercises

Slides Jan 30th

Slides Jan 16th, Time slots shortended!

Slides Jan 9th

Slides Dec 19th

Target Sequences (corrected, 20257 sequences)

CAFA rules Slides Dec 5th

Refinded slides Nov 28th HHblits Fallback

Slides Nov 21st

Target Sequences (outdated) Slides Nov 14th

Slides Nov 7th

Slides Oct 31st (updated)    Instructions

Slides Oct 24th

Data Files

Introduction