Lecture 'Protein Prediction II' WS 2011/2012

 

Type:

Lecture (4 SWS) + Exercise (2 SWS)

Ects:

8.0

Lecturer

Burkhard Rost  (lecture)
Tobias Hamp, Esmeralda Vicedo (exercise)

Rotation:

Wednesday 12:00 (st) - 13:30 (lecture)
Friday, 10:30 (st) - 12:00 (lecture)
Friday, 12:00 (ct) - 13:30 (exercise)

Place:

Lecture: Wednesday: MI 01.09.034 , Friday: MI 01.09.034 
Exercise: MI 01.09.034

Language:

English

 

Announcements:

No lecture on October 28 and November 2. Next Exercise on November 4 in room MI 01.09.034 (also see the news update). 

The videos can be downloaded on this page

Examen:

  • Makeup:

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 - 20111021 - PP2 - Burkhard Rost - "Individualized Medicine - Our Work"

Lecture 2 - 20111026 - PP2 - Burkhard Rost - "Introduction to Protein Function"

Lecture 3 - 20111109 - PP2 - Burkhard Rost - "Protein Function"

Lecture 4 - 20111111 - PP2 - Burkhard Rost - "Motifs & Function By Association"

Lecture 5 - 20111116 - PP2 - Andrea Schafferhans - "Protein Ligand Interactions Docking" 

Lecture 6 - 20111118 - PP2 - Andrea Schafferhans - "Enzymes - Predicting Function Using Structures"

Lecture 7 - 20111123 - PP2 -  Burkhard Rost  - "Predict Localization 1"

  • Video

Lecture 8 - 20111125 - PP2 - Burkhard Rost  - "Predict Localization 2"

Lecture 9 - 20111130 - PP2 - Marc Offman - "Protein Engineering 1" 

Lecture 10 - 20111202 - PP2 - Marc Offman - "Protein Engineering 2" 

Lecture 11 - 20111207 - PP2 - Andrea Schafferhans and Guy Yachdav - "Bioinformatics in Industry"

Lecture 12 - 20111209 - PP2 - Burkhard Rost - "Predict Localization 3"

Lecture 13 - 20111216 - PP2 - Tatyana Goldberg - "Predict Localization 4"

Lecture 14 - 20120111 - PP2 -  Burkhard Rost - "SNP Effect 1"

Lecture 15 - 20120113 - PP2 - Burkhard Rost -  "SNP Effect 2"

Lecture 16 - 20120118 - PP2 - Burkhard Rost - "Predict effect of mutation on function/ Predict protein-protein interactions 1"

Lecture 17 - 20120120 - PP2 - Burkhard Rost - "Predict protein-protein interactions 2"

Lecture 18 - 20120125 - PP2 - Marco de Vivo - "Paths to drug discovery and the role of computational chemistry"

Lecture 19 - 20120127 - PP2 - Marco Punta - "Pfam: what's in a protein database"

Lecture 20 - 20120201 - PP2 - Burkhard Rost - "Protein-protein interactions 3  / Protein-DNA / G0"

 

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

 

Exercise: