Arbeitsgruppe Prof. Urbassek

Biophysik 6 WS14/15 - Molekulares Modellieren


Übung am 10.12.2014 und 17.12.2014 im CIP Raum (46-306).

CIP-Account erforderlich!

Klausur: 11.02.2015


Vorlesung 1: Einführung

Vorlesung 2: Force fields und Wasser

Vorträge: 04.02.2015

  • Linda H.:
    Y. Andoh et al.: All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution.  J. Chem. Phys. 141, 165101 (2014).
  • Johannes S.:
    Nygaard et al.: The Dynamic Process of beta2-Adrenergic Receptor Activation, Cell 152, 532 (2013).
  • Tim D.:
    Karaboga, Arnaud S. et al.: Highly Specific and Sensitive Pharmacophore Model for Identifying CXCR4 Antagonists. Comparison with Docking and Shape-Matching Virtual Screening Performance. J. Chem. Inf. Model. 53, 1043 (2013).
  • Marcel J.:
    Philipp Tröster and Paul Tavan: The Microscopic Physical Cause for the Density Maximum of Liquid Water. J. Phys. Chem. Lett. 5, 138 (2014).
  • Torsten R.:
    Joshua A. Anderson, Chris D. Lorenz and A. Travesset: General purpose molecular dynamics simulations fully implemented on graphics processing units. J. Comput. Phys. 227, 5342 (2008).


Literatur zur Vorlesung:

  • A. R. Leach. Molecular modelling - principles and applications (Pearson Education Ltd., Harlow, 2001), 2. Aufl. Contains also applications on "biological systems".
  • F. Jensen: Introduction to Computational Chemistry (Wiley 2007). Focus on methods in computational chemistry. Good introductory book if you want to focus on chemistry applications
  • D. Frenkel und B. Smit. Understanding molecular simulation (Academic, San Diego, 2002), 2. Aufl. Fairly recent book. Very good background and theory on MD, MC and Stat Mech. Applications are mainly on molecular systems
  • W. Demtröder. Molekülphysik (Oldenbourg, München, 2003). For the physics of small molecules.
  • M.P. Allen and Tildesley, "Computer Simulation of Liquids", Oxford Science Publishers. (mainly MD) Excellent book on Molecular Dynamics Simulation. Explains well the relevant Statistical Mechanics. A must if you will be doing MD.
  • C. J. Cramer: Essentials of Computational Chemistry - Theories and Models (Wiley, Chichester, 2004) 2nd edition. With a focus on chemistry issues.
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