Protein Prediction II for Computer Scientists WS 2015/2016

 

Type:

Lecture (4 SWS) + Exercise (2 SWS)

Ects:

8.0

Lecturer

Burkhard Rost  (lecture)
Lothar Richter (exercise)
Juan Miguel Cejuela  (exercise)

Rotation:

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

Place:

Lecture:  MI 01.09.034

Exercise: MI 03.13.010

Exam: tba

Language:

English

Announcements:

The latest news are always on top!

NO exercise on Thursday Jan 7th as already communicated via GitHub

NO exercise on Thursday Nov 12th

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

  • Makeup: tba

Content

This lecture continues the 'Protein Prediction I' lecture. The attendance of this lecture however is not a mandatory requirement 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 27th Individual Health

Oct 29th Introfunc1 - Videos:  YouTube (1080p) , Download (360p)

Nov 3rd Introduction to Protein Function - Videos:  YouTube (1080p

Nov 12th Introduction Function Prediction 2 - Videos:  YouTube (1080p

Nov 17th CAFA - Videos:  Download (480p)

Nov 19th Localization - Videos:  YouTube Part 1 (1080p) YouTube Part 2 (1080p)  

Dec 1st Localization 2 - Videos:  YouTube (1080p)

Dec 8th Protein-Protein Interaction - No video for this lecture

Dec 10th Protein-Protein Interaction - Videos: Download (480p)

Jan 7th Drug Discovery by Marco de Vivo Slides VideoTalk

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

Jan 19th SNPs


 

Exercise

See the GitHub class repository

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Slides