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Proseminar SS 10: Selected Topics in Molecular Modelling

General Information

Lecturer: PD Dr. Michael Hutter

Dates: Thursday, June 10 and Thursday, June 17, 2:15 pm

Place: building E2 1, room 106; on June 17: room 001

Vorkenntnisse entsprechend dem 4. Studiensemester

Preliminary discussion and placement of the topics: Friday, April 16, 02:00 pm, E2 1, room 007

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

Maximum number of participants: 10+

study regulations 2006: 5

Here you can find the results.



Topics (in order of presentation):  

  1. Force Fields: Atom types, force fields for proteins, DNA, organic and inorganic compounds: AMBER, CHARMM, MM3, UFF
  2. Partial Atomic Charges: Concepts and use in force fields, electronegativity, Gasteiger-Marsili charges, Electrostatic potential derived charges, constraints, differences in the CHARMM, AMBER, and MM2 force fields.
  3. Minimization Algorithms: local, global, with and whithout the use of gradients, DFP, eigenvector following, simplex, simulated annealing, genetic algorithms (10.06.)
  4. Solvent Models in Force Fields: explicit and implicit water models, OPLS force field, Generalized Born Model, Poisson-Boltzmann, Ewald Summation.
  5. Scoring Functions for Docking: Energy-based vs. knowledge-based scoring, estimation of entropic contributions and desolvation, DrugScore, consensus scoring. (10.06.)
  6. Conformational Search: conf. space, systematic search, tree search, random and stochastic search, distance geometry.
  7. Interpreting X-ray Structures of Proteins: The .pdb file format, resolution, temperature factors, synchrotron scattering, crystal cells. (17.06.)
  8. Generation of 3D Molecular Structures: 3D coordinates from scratch, CORINA (17.06.)
  9. Additional topics to be announced


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