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Pro-/Seminar WS 07/08: Current Topics in Bioinformatics

General Information

Lecturer: Prof. Dr. Volkhard Helms

Tutors: Susanne Eyrisch, Wei Gu, Barbara Hutter, Peter Walter

Time: March 4 - 6, 2 pm - 6 pm, building B2 1, room 312
Proseminar: Vorkenntnisse entsprechend dem 4. Studiensemester
Seminar: Vorkenntnisse entsprechend dem Umfang des Bachelorstudiums/Knowledge corresponding to the bachelor course


Preliminary discussion and placement of the topics: Thursday, October 25, 4:30 pm, building C7 1, room 1.08 

Condition for certification: successful presentation, regular (≥ 75 %) participation.

Maximum number of participants: 12

study regulations 2006: 5 (proseminar) or 7 (seminar)
study regulations 2004: 5 (proseminar) or 8 (seminar)
study regulations 2001: 9 (proseminar and seminar)


Possible Topics are: 

  1. Properties of Binding Pockets    (Seminar Talk by Sabine Müllerr)
    Compare the properties (volume, polarity) of binding pocket in the free protein, the protein with bound ligand, and the protein with bound inhibitor program (BALLPass and a set of structures will be provided)
    Brady, G.P., Stouten, P.F.W. Fast prediction and visualization of protein binding pockets with PASS. J. Comput. Aided Mol. Des. (2000), 14, 383-401. 
    Wang, R., Fang, X., Lu, Y., Yang, C.-Y., Wang, S. The PDBbind Database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J. Med. Chem. (2004), 47, 2977-2980.
    Wang, R., Fang, X., Lu, Y., Yang, C.-Y., Wang, S. The PDBbind database: Methodologies and updates. J. Med. Chem. (2005), 48, 4111-4119.
  2. Prediction of Protein Motions (Proseminar Talk by Christin Wolf)
    Use the programs CONCOORD/DYNAMITE to predict conformations and concerted motions of the GYF-domain (1L2Z) and of MDM2 (1YCR)
    de Groot, B.L., van Aalten, D.M.F., Scheek, R.M., Amadei, A., Vriend, G., Berendsen, H.J.C. Prediction of protein conformational freedom from distance constraints. Proteins (1997), 29, 240-251.
    Barrett, C.P., Hall, B.A., Noble, M.E.M. Dynamite: A simple way to gain insight into protein motions. Acta Crystallographica (2004), 60, 2280-2287.
  3. Disordered Regions (Proseminar Talk by Marc Thobae)
    Use the webserver DISOPRED2 to predict disordered regions in transcription factors (1D66, 1GT0, 1UBD, 1A3Q, 1BL0)
    Ward, J.J., Sodhi, J.S., McGuffin, L.J., Buxton, B.F., Jones, D.T. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. JMB (2004), 337, 635-645.
  4. DNA sequence analysis tools for the identification of regulatory motifs: Identification of tandem repeats (Seminar Talk by Cedric Laczny)
    Tandem repeats are a special case of repetitve sequences in genomes. They are involved in DNA structure and gene regulation. The Tandem repeats finder (1) applies a probabilistic model to detect tandem repeats. Besides illustrating the algorithm, the results of using the program with different parameters on selected human genomic sequences are to be reproduced as presented in the paper.
    (1) Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research (1999), 27 (2), 573-580.
  5. DNA sequence analysis tools for the identification of regulatory motifs: Identification of CpG islands (Proseminar Talk by Matthias Bieg)
    CpG islands are indicative of reduced DNA methylation. They are frequently found at the transcriptional start sites of vertebrate genes. The traditional sliding window method of the CpG island searcher (2) and the recursive segmentation approach for CpG island detection (3) are to be compared with respect to their algorithms and the results obtained for the human genomic sequence AL022237 as an example.
    (1) Takai, D., Jones, P.A. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc. Natl. Acad. Sci. USA (2002), 99 (6), 3740-3745. 
    (2) Li, W., Bernaola-Galvan, P., Haghighi, F., Grosse, I. Applications of recursive segmentation to the analysis of DNA sequences. Computers & Chemistry (2002), 26 (5), 491-510.
  6. DNA sequence analysis tools for the identification of regulatory motifs: Identification of transcription factor binding sites by comparative genomics (Seminar Talk by Siba Ismael)
    Gene regulatory elements like putative transcrition factor binding sites can be easily detected as conserved regions in pairwise sequence alignments (4, 5). The pipeline of transcription factor binding site detection at the Comparative Genomics Center (4) is to be explained in detail (BLASTZ algorithm, definition of PWM) and illustrated by an exemplary analysis (e.g. of pig AY044828 and the orthologous human genomic sequence).
    (4) Loots, G.G., Ovcharenko, I. rVISTA 2.0: evolutionary analysis of transcription factor binding sites. Nucleic Acids Research (2004), 32 (Web Server Issue), W217-W221.
    (5) Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D., Miller, W. Human-mouse alignments with BLASTZ. Genome Research (2003), 13 (1), 103-107. Miller Lab.
  7. Analyze a molecular dynamics (MD) trajectory: (Seminar talk by Peter Schüffler) compute RMSD and RMSF (the trajectory will be superimposed to the starting conformation before giving to the student, the format of the trajectory can be pdb, gro...). The student should write his/her own script, with options to choose the atoms (e.g. all atoms, all backbone atoms, all Cα atoms, loop, etc). After that, he/she should compare his/her result with those obtained from analysis tools in GROMACS. The results should be presented as plots.
  8. Modeling short peptides with different secondary structures (Seminar talk by Hai Chi) (extended loop, α-helix, β-sheet...) using the program TINKER. Optimize the modeled structures using the Minimize tool in TINKER with/without implicit solvent model. Point out the differences between the optimized structure using /not using solvent model and give explanations for these differences.
    (other option: instead of discussing the differences, you may also calculate the total number of hydrogen bonds in each conformation using their own script)
  9. Write a small program to compute the contact maps of several (at least two) conformations of a protein  (or several proteins). (Proseminar Talk by Erik Bernstein) The contact map should distinguish the strength of the contacts (e.g. base on the distance between the center of mass of the side chains of each contact pair). The results should be presented as plots.
  10. Relationship between function determined by Gene ontology and features of proteins (Proseminar Talk by Thomas Prätzlich)
  11. Distinction between obligate and non-obligate interfaces (Seminar Talk by Naharajan L.)
    put sequential and structural data about obligate and non-obligate interfaces into a self designed database
  12. Conservation of protein interface residues (Proseminar Talk by Hanna Lorig)
    • compare conservation between interface and non-interface residues with the ConSurf webserver
    • usage of programming language is optional
    • papers:
      Landau, M., Mayrose, I., Rosenberg, Y., Glaser, F., Martz, E., Pupko, T., and Ben-Tal, N. Identification of functional regions in proteins by surface-mapping of Phylogenetic information. Nucl. Acids Res. (2005), 33, W299-W302.
      Caffrey, D.R., Somaroo, S., Hughes, J.D., Mintseris, J., and Huang, E.S. Are protein-protein interfaces more conserved in sequence than the rest of the protein surface? Protein Science, 13, 190-202.
  13. Application of ant colony optimization to structure-based drug design (Proseminar Talk by Jan-Malte Hoinka)
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