Protein Prediction II for Computer Scientists 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, 11:00 - 12:30 (lecture)
Thursday, 11:00 - 12:30 (lecture)
Thursday, 12:30 - 13:30 (exercise)

 

 

Place:

Lecture: Tuesday: FMI 01.09.034, Thursday: FMI 01.09.034

Exercise: Thursday: FMI 01.09.014

Exceptions: on Dec 5th and Dec 19th in FMI 00.09.038

Exam: 00.12.019 see also below in Announcements

Language:

English

 

Announcements:

The latest new is always on top! Please check out frequently since on the semester beginning there always can be changes on short notice.

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

Examination will take place in room 00.12.039 (Faculty Room) on Tue Feb 4th  between 11-13 o'clock.

No lecture and 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

The room numbers has changed. Please see above. For exercise we will have a new room soon.

Please note: The first lecture in the winter semester 2013/14 will take place on Thursday, October 17th, in room MW 2050 (Boltzmannstr. 15).

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 

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

Lecure 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 (Video)

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

No lecture slide on Jan 7th

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

Lecture slides Jan. 14th.  Protein Protein Interaction 2 cont'd / Protein Protein Interaction 3 (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)

Lecture slides Jan. 28th SNP (Video)

Exercises

Slides Jan 30th

Slides Jan 16th

Slides Jan 9th

Slides Dec 19th

Target Sequences (corrected, 20257 sequences)

CAFA rules Slides Dec 5th

Refined slides Nov 28th     HHblits Access

Slides Nov 21st

Target Sequences (outdated) Slides Nov 14th

Slides Nov 7th

Slides Oct 31st (updated)   Instructions (new)

Slides Oct 24th

Data Files

Introduction