Proseminar 'Proteins and Disease' SS 2012

Type:            Seminar (2 SWS)
Ects:             4.0
Lecturer:      Burkhard Rost
Time:           Monday, 13:30 - 15:00
Room:          MI 01.09.034
Language:    English

 Content

 Topics related to the research interests of the group: protein sequence analysis, sequence based predictions, protein structure prediction and analysis; interaction networks.

 Pre-meeting

February 16, 2012 , 13:30
The rules and hints for preparation of the seminar that were given in the pre-meeting are also summarised in our Checklist.

Schedule

April 16   Vanessa Schmoll: Protein Structure
              Advisor: Marc Offman

April 23   Carolin Prexler: Biological Databases
              Advisor: Esmeralda Vicedo

April 30   Tobias Lutzenberger: Protein structure classification
              Advisor: Edda Kloppmann

May 7     Jonas Raedle: Integral membrane protein structures and their classification
              Advisor: Edda Kloppmann

May 14    Angela Hempfer: Sequence alignment: local and global
              Advisor: Andrea Schafferhans

May 21    Yvonne Awaloff: Sequence alignment and searches: heuristic methods
              Advisor: Laszlo Kajan

June 4     Double session!
               Evelyn Kirner: Sequence searches using profiles (PSI-Blast et al.)
              Advisor: Maximilian Hecht
              Susanne Brunner: Monte Carlo methods
              Advisor: Edda Kloppmann

June 11   Ehet Benjamin: Multiple sequence alignment
              Advisor: Maximilian Hecht

June 18   Tim Jeske: Short Sequence Motifs
              Advisor: Tobias Hamp

June 25   Benjamin Schmidt: Protein secondary structure prediction
              Advisor: Christian Schäfer

July 2      Anton Smirnov: Homology modelling
              Advisor: Andrea Schafferhans

July 9      Marco Lombardi: Biological Networks
              Advisor: Tobias Hamp

July 16    Maria Schelling: Phylogenetic Prediction
              Advisor: Esmeralda Vicedo

Topics

Protein structure

Marc Offmann

This talk shall review protein structure, the physics determining protein folding and structural elements stabilising proteins.

Literature:

tba.

 

Protein structure classification

Dr. Edda Kloppmann

Protein structures are classified for example in the databases SCOP and CATH. Secondary structure elements provide a first, simple and very important structural classification. Secondary structure predictions for proteins without known structure are used in a large variety of applications.This talk shall give an introduction to the different levels of protein structure (primary, secondary, tertiary and quaternary) and to protein structure classification.

Literature:

  • Arthur M. Lesk. Introduction to bioinformatics.
  • Alberts et al. Molecular biology of the cell.

Integral membrane protein structures and their classification

Dr. Edda Kloppmann

The important class of integral membrane proteins (IMPs) provides the link between cell and environment or between different cell compartments and is for example involved in ion transport, signaling and cell adhesion. Structures of these proteins are particularly difficult to solve. Nevertheless, a significant number of structures is known today. This talk shall give an introduction to IMP structure and their orientation in the membrane which has to be calculated.

Literature:

  • Alberts et al. Molecular biology of the cell.
  • Lomize et al. (2006) Positioning of proteins in membranes: A computational approach. Protein Science 15: 1318-1333. (A good introduction can also be found on the website: opm.phar.umich.edu.)
  • Tusnády et al. (2005) TMDET: web server for detecting transmembrane domains by using 3D structure of proteins. Bioinformatics 21: 1276-1277

Monte Carlo methods

Dr. Edda Kloppmann

Monte Carlo methods use random sampling for computation. These methods were first used in the 1940s and are still widely applied to obtain predictions for biological systems.

Biological Databases

Dipl. Biol. Esmeralda Vicedo

Huge volumes of primary data are archived in numerous open-access databases, and with new generation technologies becoming more common in laboratories. This seminar shall give an overview of different Databases, how to access them and problems associated.

  • Arthur M. Lesk. Introduction to bioinformatics (Third Edition) Oxford University Press

Sequence alignment: local and global

Dr. Andrea Schafferhans

Finding an alignment of two protein sequences is the basis of all techniques to infer knowledge by homology. This talk shall review well-known local and global alignment methods (Smith-Waterman, Needleman-Wunsch).

Literature:

Sequence alignment and searches: heuristic methods

Laszlo Kajan

This talk shall explain the heuristic approximations made to speed up sequence alignment and sequence searches (BLAST, FASTA).

Literature:

tba

Sequence searches using profiles (PSI-Blast et al.)

Maximilian Hecht

This talk shall explain why and how profiles help in searching sequence databases and how the profile searches work technically.

Literature:

Multiple sequence alignment

Maximilian Hecht

This talk shall explain the methods used to generate multiple sequence alignments, the complexity of the problem and the approximations made.

Literature:

  • A.M Lesk Bioinformatik: Eine Einführung. Spektrum Akademischer Verlag, 2002.
  • Thompson JD, Higgins DG, Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.Nucleic Acids Res 22: 4673–4680.
  • Edgar RC (2006). Multiple Sequence Alignment. Curr opin struct biol 16: 368-373.
  • http://en.wikipedia.org/wiki/Multiple_sequence_alignment

 

Short Sequence Motifs

Tobias Hamp

Short sequence motifs are reoccurring patterns that are functionally important. Here, we want to give an introduction where and how they play a role, how we can find them and what we know so far.

Literature:

  • Patrik D'haeseleer: What are DNA sequence motifs?, Nature Biotechnology, 24(4): 423-425 (2006)
  • Bailey TL, Elkan C.: Fitting a mixture model by expectation maximization to discover motifs in biopolymers, Proc Int Conf Intell Syst Mol Biol, 2:28-36. (1994),

  

Protein secondary structure prediction

Dipl. Bioinf. Christian Schaefer

Predicting the secondary structure elements comes into play when only the sequence of a protein is known. In this seminar, an overview and discussion shall be given of both historical and more recent approaches.

Literature:

  • David Mount, Bioinformatics - Sequence and Genome Analysis (Second Edition), Cold Spring Harbor Laboratory Press

Homology modelling

Dr. Andrea Schafferhans

If the structure of a protein has not been resolved experimentally, one can often model the sequence by homology to other sequences. This seminar shall give an overview of homology modelling techniques.

Literature:

 

Biological Networks

Tobias Hamp

In biochemistry, both experimental and predicted data is often represented in the form of networks. This seminar is supposed to give an overview of their various types in terms of differences, commonalities and applications.

Literature:

  • Marc Vidal, Michael E. Cusick, Albert-László Barabási, Interactome Networks and Human Disease, Cell, 144(6): 986-998,

Phylogenetic Prediction

Dipl. Biol. Esmeralda Vicedo

Variations within a family of related nucleic acid or protein sequences provide an inestimable source of information for evolutionary biology. In this topic we will have an overview of the procedures for phylogenetic analysis, concepts and methods.

Literature:

  • David Mount, Bioinformatics - Sequence and Genome Analysis (Second Edition), Cold Spring Harbor Laboratory Press