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Special-topic Lecture Bioinformatics: Membrane Bioinformatics

General Information

Lecturers: Prof. Dr. Volkhard Helms, Dr. Rainer Böckmann

Tutor: Sikander Hayat

Time: Monday, 10:15 am - 11:45 am, building E1 4, seminar room 0.21
Tutorial: after the lecture, same room, ca. every 2 weeks

Requirements: knowledge according to Bioinformatics I and II, programming experience e.g. in Python

Condition for certification: at least 50% of points from 4 assignments, final oral exam

Leistungspunkte/Credit points: 5 (V2/Ü1)

This course is taught in English language.

Topics to be covered:

  • Composition of biological membranes
  • Membrane properties: electrostatics, diffusion of lipids and proteins, phase transition liquid/crystalline
  • Sequence-based identification of membrane proteins and transmembrane segments
  • Predicting structural features of helical and beta-barrel proteins: secondary structure, lipid exposure
  • Classification of membrane proteins

The lecture introduces the students to biological phospholipid bilayers and their biophysical properties. On the example of transmembrane proteins, we will discuss various important topics of current bioinformatics: pattern identification, machine learning, and methods from structural bioinformatics such as continuum electrostatics and Metropolis Monte-Carlo.

Assignments:

4 assignments will be given out to be completed within 2 weeks each:

  • Pattern identification
  • Detecting secondary structure elements with a Hidden Markov Model
  • Continuum electrostatics: Born equation, Gouy-Chapman law, Poisson-Boltzmann equation solver
  • Monte Carlo simulation of lipid diffusion in 2 dimensions.

 

Lecture 1: April 27 ppt pdf
Lecture 2: May 4
ppt
pdf

Lecture 3: May 11 ppt
pdf
Assignment 1
Lecture 4: May 18 ppt
pdf
This lecture takes places on Wednesday, May 20,
2:00 pm - 4:00 pm, in building E1 1, room 407
Lecture 5: May 25 ppt
pdf
Assignment 2
Lecture 6: June 8 ppt
pdf

Lecture 7: June 15 ppt
pdf
This lecture takes place on Thursday, June 18,
4:00 pm - 6:00 pm, in building E2 5, room H 04 (SR 2)
Lecture 8: June 22

This lecture takes place on Friday, June 26,
2:00 pm - 4:00 pm, in building E2 5, room S2 (H 04)
Lecture 9: June 29 ppt
pdf

Lecture 10: July 6 ppt
pdf

Lecture 11: July 13

Assignment 3
Lecture 12: July 20


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