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.
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 Lukas Friedrich: 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
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
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
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
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