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Pro-/Seminar: Current Topics in Molecular Modelling

General Information

Lecturer: PD Dr. Michael Hutter

Dates: Thursday, 04:00 pm - 06:00 pm on November 17 (#1, #2) and 24 (#3, #4), December 1 (#5, #6), 8 (#7, #8), and 15 (#9, #10), January 12 (#11, #12)

Place: building E2 1, room 007

Vorkenntnisse entsprechend dem 4. Studiensemester; Knowledge corresponding to semester 4

Preliminary discussion and placement of the topics: Friday, October 21st, 16:15, building E2 1, room 0.07

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

Maximum number of participants: 12

study regulations 2006: 5 (proseminar) or 7 (seminar)




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
  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.
  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.
  8. Generation of 3D Molecular Structures: 3D coordinates from scratch, CORINA, CONCORD, knowledge-based approaches.
  9. Superpositioning of molecules: Optimum alignment of (rigid) 3D-structures, Kapsch algorithm, RMSD and other distance criteria.
  10. Assigning hydrogens to molecules, protonation states: general rules for valencies, titratable groups, change of protonation state due to interactions within a binding pocket.
  11. Hydrogen-bond networks in proteins: Finding the optimal interactions between protein residues, flip of side chains within proteins, assigning of corresponding polar hydrogens to X-ray structures. Comparison with the programs GRID and WHATIF.
  12. Maximum common substructure: Clique detection, colored graphs, reduced graphs.


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