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Seminar SS 09: Selected Topics in Molecular Modelling

General Information

Lecturer: PD Dr. Michael Hutter

Time: Friday, June 5, June 26, July 3 and July 10, 2:00 pm - 5:00 pm, building E1 3, room 0.16

Requirements: Seminar topics, only (45 min talk + discussion). Knowledge corresponding to the bachelor course, esp. Computational Chemistry.

Preliminary discussion and placement of the topics: Tuesday, April 28, 5:00 pm, building C7 1, room 1.08

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

Maximum number of participants: 8

study regulations 2006: 7
study regulations 2004: 8

 Topics (in order of presentation):  

  1. Force Fields: Atom types, force fields for proteins, DNA, organic and inorganic compounds: AMBER, CHARMM, MM3, UFF
  2. Prediction Methods for logP: fragment-based and atom type-based additive contributions, correction factors, application of machine learning algorithms e.g. neural networks, various approaches like ClogP, XlogP. How many parameters are required?
  3. Molecular Descriptors: concepts, 1D, 2D, 3D-descriptors, topological, similarity indices and measurements, CoMFA
  4. Generating Partial Atomic Charges: electrostatic potential derived charges, RESP, CHELP/G, Gasteiger-Marsili charges, electronegativity, small vs. large molecules.
  5. Encoding Molecular Structures: unique representation of molecules, canonical SMILES, InChI, online-translators
  6. Generation of 3D Molecular Structures: 3D coordinates from scratch, CORINA
  7. In silico Drug Development: Lipinski’s rule of five, drug-likeness criteria of Oprea, Wendolowski et al., leadlike vs. druglike
  8. Hydrogen-Bond Networks in Proteins: assignment, treatment of lone pair electrons of water in the YETI force field and the GRID program, flip of side chains, correcting and optimizing atom positions in crystallographic files, WHATIF.
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