Prospectus

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molecular modelling

Course 2014-2015

Molecular modeling is an exciting new approach to a wide variety of problems in chemistry. In this course we address problems in drug design, drug delivery and supra-molecular chemistry. Students will learn how to set up, run and analyze a model. We cover a range of techniques: Quantitative Structure Activity Relations, Molecular Patterns, (Semi-Empirical) Quantum Chemistry, and various variants to Molecular Dynamics and Mixing Thermodynamics. Applications include: how to generate organic molecules, peptides and proteins, bilayers, and composite biomaterials, and how to model protein ligand binding from a Keratine binding database. An important element of the course is extensive hands-on modeling using advanced software tools. The final assignment will include a model for the solubility delivery of Taxol, an important anti-cancer medicine (cytostatic).

The student should have an interest in theory and computer simulations, with a good background in mathematics and statistical thermodynamics, and preferably should have followed the course STD, statistische thermodynamica, (Dr. Blokhuis) before

Study Goals: To understand the basic principles of programming, and molecular modeling.
Education Method: The course is divided between oral lectures in the morning and hands-on computer simulations and exercises in the afternoon.
Assessment: Take-Home exercises and final assignment.
Enrolment / Application Send email to j.fraaije@chem.leidenuniv.nl, or blackboard.