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Pro-/Seminar:
Konformationssampling beim strukturbasierten Drug Design

Winter Semester 06/07


Lecturer: Prof. Dr. Volkhard Helms

Tutors: Susanne Eyrisch, Wei Gu

Time: Friday, Dec. 8, Dec. 15, Jan. 19, Jan. 26, Feb. 2, 2:15 pm, building E1 4 (MPI), room 0.23

Requirements:
Proseminar: Vorkenntnisse entsprechend dem 4. Studiensemester
Seminar: Vorkenntnisse entsprechend dem Umfang des Bachelorstudiums

Start: to be announced

Preliminary discussion and placement of the topics: Tuesday, October 17, 2006, 4:15 pm, building C7 1, room 1.08

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

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

Order of Presentation

Possible Topics are:

    Topic 1: MD/MC and Force Field Vortrag Xavier Mol
    Topic 2: Umbrella Sampling and Multicanonical Methods
    Topic 3: Multi-Copy/Conformational Ensemble (Proseminar)
    Topic 4: LES (Local Enhanced Sampling)
    Topic 5: Force probe MD
    Topic 6: Potential of mean force
    Topic 7: Free energy calculation (MCTI/FEP)
    Topic 8: Free energy calculation (MMPBSA)
    Topic 9: Implicit solvent model (GBSA)
    Topic 10: Multi-replica Simulations
    Topic 11: Protein-protein Docking Vortrag Sabine Müller
    Topic 12: Protein flexibility predictions using graph theory Vortrag Jan Christoph
    Topic 13: Hammerhead Vortrag Oliver Frings
    Topic 14: Raptor
    Topic 15: Poling
    Topic 16: A*-Search Handout Daniel Primaveßy
    Topic 17: Dead-end Elimination
    Topic 18: Stochastic Roadmap Simulation
    Topic 19: Systematically Applied Local Perturbations
    Topic 20: MacroModel Vortrag Lisa Blaß