Arbeitsgruppe Prof. Urbassek

Biophysik 6 - Molekulares Modellieren


Übung am 09. und 16. Januar 2013 im CIP Raum (46-306).

CIP-Account erforderlich!


Vorlesung 1: Einführung

Vorlesung 2: Force fields und Wasser

Übung 1: Einführung in Linux und VMD

Übung 2: MD-Simulation


(16.01 bzw. 30.01.2013)

  • Andreas H.:
    Jarek Juraszek, Jocelyne Vreede, Peter G. Bolhuis: Transition path sampling of protein conformational changes, Chemical Physics 396 (2012) 30–44
  • Alena L.:
    Li Na Zhao, See-Wing Chiu, Jerome Benoit, Lock Yue Chew, and Yuguang Mu: Amyloid β Peptides Aggregation in a Mixed Membrane Bilayer: A Molecular Dynamics Study, J Phys Chem B 115 (2011) 12247
  • Veronika C.:
    T. Hirschberger, M Stork, B Schropp, KF. Winklhofer, J Tatzelt, and P Tavan (2006). Structural instability of the prion protein upon M205S/R mutations revealed by molecular dynamics simulations. Biophys. J. 90 (2006) 3908
  • Sebastian S.:
    Hetenyi, C. and van der Spoel, D.: Blind docking of drug-sized compounds to proteins with up to a thousand residues. FEBS Lett. 580 (2006) 1447
    HTML, PDF, Suppl. Material
  • Laurien H.:
    Bert L. de Groot, Andreas Engel, Helmut Grubmüller: A  refined structure of human aquaporin-1. FEBS Lett.504  (2001) 206
  • Maria L.:
    Francesco Paesani and Gregory A. Voth: The Properties of Water: Insights from Quantum Simulations, J Phys Chem B 113 (2009) 5702
  • Tatjana M.:
    Francesco Paesani and Gregory A. Voth: The Properties of Water: Insights from Quantum Simulations, J Phys Chem B 113 (2009) 5702
  • Fabian D.:
    Ole G. Mouritsen et al: Random-Lattice Simulations of Biomembranes. In Computational Soft Matter: From Synthetic Polymers to Proteins (2004).
  • Alexander N.:
    Bondar et al.: Key role of electrostatic interactions in bacteriorhodopsin proton transfer. JACS 126 (2004) 14668
  • Markus F.:
    Robert R. Johnson,A. T. Charlie Johnson and Michael L. Klein: Probing the Structure of DNA−Carbon Nanotube Hybrids with Molecular Dynamics . Nano Letters 2008 8 (1), 69-75
    HTML, PDF, Supporting info
  • Simon P.:
    Marti-Renom M.A., Stuart,A.C., Fiser,A., Sanchez,R., Melo,F. and Sali,A. (2000) Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct., 29, 291–325.


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. Moleküphysik (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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