Publications

Publications, Talks and Posters of Dr. Frank Beierlein

Publications from FAU Current Research Information System (CRIS)

2016

2015

2013

2012

2011

2007

2006

2004

2003

 

Publications

  • Frank Beierlein, Harald Lanig, Gudrun Schürer, Anselm H. C. Horn and Timothy Clark
    Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: An Evaluation for Known Test Systems
    Mol. Phys. 2003, 101, 2469-2480. (DOI: 10.1080/0026897031000092940)
  • Olaf G. Othersen, Frank Beierlein, Harald Lanig and Timothy Clark
    Conformations and Tautomers of Tetracycline
    J. Phys. Chem. B 2003, 107, 13743-13749. (DOI: 10.1021/jp0364506)
  • Frank Beierlein and Timothy Clark
    Computer Simulations of Enzyme Reaction Mechanisms: Simulation of Protein Spectra
    in High Performance Computing in Science and Engineering, Munich 2004 – Transactions of the Second Joint HLRB and KONWIHR Status and Result Workshop, March 2-3, 2004, Technical University of Munich and Leibnitz-Rechenzentrum Munich, Germany (Eds.: S. Wagner, W. Hanke, A. Bode, F. Durst)
    Springer-Verlag, Berlin, Heidelberg, New York, 2004, pp. 245-260.
  • Frank Beierlein
    QM/MM Docking and Simulations of FRET
    PhD thesis, Universität Erlangen-Nürnberg, Erlangen, 2005.
  • Frank R. Beierlein, Olaf G. Othersen, Harald Lanig, Siegfried Schneider and Timothy Clark
    Simulating FRET from Tryptophan: Is the Rotamer Model Correct?
    J. Am. Chem. Soc. 2006, 128, 5142-5152. (DOI: 10.1021/ja058414l)
  • Harald Lanig, Olaf G. Othersen, Frank R. Beierlein, Ute Seidel and Timothy Clark
    Molecular Dynamics Simulations of the Tetracycline-Repressor Protein: The Mechanism of Induction
    J. Mol. Biol. 2006, 359, 1125–1136. (DOI: 10.1016/j.jmb.2006.04.014)
  • Harald Lanig, Olaf G. Othersen, Ute Seidel, Frank R. Beierlein, Thomas Exner and Timothy Clark
    Structural Changes and Binding Characteristics of the Tetracycline-Repressor Binding Site on Induction
    J. Med. Chem. 2006, 49, 3444-3447. (DOI: 10.1021/jm060289g)
  • Ute Seidel, Olaf G. Othersen, Harald Lanig, Frank R. Beierlein and Timothy Clark
    Molecular Dynamics Characterization of the Structures and Induction Mechanisms of a Reverse Phenotype of the Tetracycline Receptor
    J. Phys. Chem. B 2007, 111, 6006-6014. (DOI: 10.1021/jp0674468)
  • Frank R. Beierlein, Julien Michel and Jonathan W. Essex
    A Simple QM/MM Approach for Capturing Polarization Effects in Protein-Ligand Binding Free Energy Calculations
    J. Phys. Chem. B 2011, 115, 4911-4926. (DOI: 10.1021/jp109054j)
  • Frank R. Beierlein, G. Geoff Kneale and Timothy Clark
    Predicting the Effects of Basepair Mutations in DNA-Protein Complexes by Thermodynamic Integration
    Biophys. J. 2011, 101, 1130-1138. (DOI: 10.1016/j.bpj.2011.07.003)
  • Gül Altınbaş Özpınar, Frank R. Beierlein, Wolfgang Peukert, Dirk Zahn and Timothy Clark
    (Gül Altınbaş Özpınar and Frank R. Beierlein contributed equally to this work)
    A Test of Improved Force Field Parameters for Urea: Molecular-Dynamics Simulations of Urea Crystals
    J. Mol. Model. 2012, 18, 3455-3466. (DOI: 10.1007/s00894-011-1336-5)
  • Frank R. Beierlein, Andreas M. Krause, Christof M. Jäger, Piotr Fita, Eric Vauthey and Timothy Clark
    Molecular Dynamics Simulations of Liquid Phase Interfaces: Understanding the Structure of the Glycerol/Water-Dodecane System
    Langmuir 2013, 29, 11898-11907. (DOI: 10.1021/la4021355)
  • Frank R. Beierlein, Timothy Clark, Björn Braunschweig, Kathrin Engelhardt, Lena Glas and Wolfgang Peukert
    Carboxylate Ion-Pairing with Alkali-Metal Ions for Beta-Lactoglobulin and Its Role on Aggregation and Interfacial Adsorption
    J. Phys. Chem. B 2015, 119, 5505-5517. (DOI: 10.1021/acs.jpcb.5b01944)
  • Frank R. Beierlein,* Miguel Paradas Palomo, Dmitry I. Sharapa, Oleksii Zozulia, Andriy Mokhir and Timothy Clark
    DNA-Dye-Conjugates: Conformations and Spectra of Fluorescence Probes
    PLoS ONE 2016, 11(7), e0160229. (DOI: 10.1371/journal.pone.0160229)

Talks

  • Frank Beierlein, Tim Clark
    Simulating the Induced Fit: A Combined QM/MM Docking Approach
    MGMS Young Modellers’ Forum in Conjunction with the RSC MMG, London, November 30, 2001.
  • Frank Beierlein, Tim Clark
    A QM/MM Docking Approach with a Flexible Protein Environment
    16. Darmstädter Molecular Modelling Workshop, Darmstadt, May 7-8, 2002.
  • Harald Lanig, Frank Beierlein, Olaf Othersen, Siegfried Schneider, Timothy Clark
    Combining Molecular Dynamics Simulations with Semiempirical CI-Calculations to Investigate Fluorescence Resonance Energy Transfer (FRET) within the Tetracycline Repressor
    43rd Sanibel Symposium, St. Augustine, Florida, February 22-March 1, 2003.
  • Frank Beierlein, Harald Lanig, Olaf Othersen, Siegfried Schneider, Timothy Clark
    An MD/CI Approach for the Investigation of Fluorescence Resonance Energy Transfer in Proteins
    17. Darmstädter Molecular Modelling Workshop, Erlangen, May 27-28, 2003.
  • Frank Beierlein, Harald Lanig, Olaf Othersen, Siegfried Schneider, Timothy Clark
    An MD/CI-approach simulating FRET in proteins
    227th ACS National Meeting, Anaheim, CA, March 28-April 1, 2004.
  • Anselm H. C. Horn, Frank Beierlein, Harald Lanig, Gudrun Schürer, Timothy Clark
    Quantum mechanical/molecular mechanical (QM/MM) docking: A new protocol and its evaluation for known test systems
    227th ACS National Meeting, Anaheim, CA, March 28-April 1, 2004.
  • Frank Beierlein, Olaf Othersen, Timothy Clark, Harald Lanig
    A Molecular Dynamics/Configuration Interaction (MD/CI)-Approach Simulating FRET in Proteins
    eCheminfo 2004 “Applications of Cheminformatics and Chemical Modelling to Drug Discovery”, November 8-19, 2004.
  • Frank Beierlein, Jon Essex
    Free Energy Studies of MAO-B
    IntBioSim Project Meeting, UCL, London, February 1-2, 2007.
  • Frank Beierlein, Jon Essex
    Correcting MM-Monte Carlo Energies by QM/MM Calculations
    IntBioSim Project Meeting, University of Oxford, Oxford, July 2-3, 2007.
  • Frank R. Beierlein, Olaf G. Othersen, Harald Lanig, Siegfried Schneider, Timothy Clark
    Understanding FRET Experiments for the Tetracycline Repressor
    EBSA Satellite meeting – Computational Biophysics: linking experiment and theory, Imperial College, London, July 19, 2007.
  • Frank Beierlein, Jon Essex
    QM/MM Binding Free Energy Calculations
    SWCC07, Cardiff University, Cardiff, Sept 26, 2007.
  • Frank Beierlein
    Protein-Ligand Binding Free Energy Calculations: From Classical MC to QM/MM
    Gemeinsames Seminar der Theoretischen Chemie und des Computer-Chemie-Centrums, Universität Erlangen-Nürnberg, Erlangen, Dec 17, 2007.
  • Frank Beierlein
    Current applications of QM/MM: FRET and Free Energy Calculations
    Gemeinsames Seminar der Theoretischen Chemie und des Computer-Chemie-Centrums, Universität Erlangen-Nürnberg, Erlangen, May 19, 2008.
  • Frank Beierlein
    Understanding FRET Experiments for the Tetracycline Repressor
    2. Fränkisches Theoretikertreffen, Universität Würzburg, Würzburg, Nov 19-20, 2009.
  • Andreas Krause, Frank Beierlein, Christof Jäger, Piotr Fita, Eric Vauthey, Tim Clark
    Understanding the Fine Structure of Liquid-Liquid Interfaces
    27th Molecular Modeling Workshop, Erlangen, Feb 25-27, 2013.
  • Frank Beierlein
    Aggregation and Self-Organization of Flexible Molecules
    EAM Winter School I, Kirchberg/Tirol, Mar 11-14, 2013.

Posters

  • Frank Beierlein, Harald Lanig, Gudrun Schürer, Anselm Horn and Tim Clark
    Simulating the Induced Fit: A Combined QM/MM Docking Approach
    Model(l)ing 2001, The Annual International Meeting of the Molecular Graphics and Modelling Society, Erlangen, September 17-21, 2001.
  • Jürgen Bulitta, Franz Schönfeld, Frank Beierlein, Harald Lanig, Timothy Clark and Reinhard Troschütz
    Chiral structure separation for drug synthesis: Docking of methotrexate and derivatives into the dihydrofolate reductase (DHFR) binding site
    17. Darmstädter Molecular Modelling Workshop, Erlangen, May 27-28, 2003.
  • Frank Beierlein, Harald Lanig, Olaf Othersen, Siegfried Schneider, Timothy Clark
    Simulating Fluorescence Resonance Energy Transfer: A Combined Molecular Dynamics-QM/MM-CI Approach
    45th Sanibel Symposium, St. Simons Island, GA, March 5-11, 2005.
  • Frank Beierlein, Olaf G. Othersen, Harald Lanig, Siegfried Schneider and Tim Clark
    Simulating FRET: A Combined Molecular Dynamics-QM/MM Approach
    19. Darmstädter Molecular Modelling Workshop, Erlangen, May 3-4, 2005.
  • Frank Beierlein, Jonathan Essex
    QM/MM Binding Free Energy Calculations
    Biomolecular Simulation 2008, Bristol, Jan 7-9, 2008.
  • Frank Beierlein, Jonathan Essex
    QM/MM Binding Free Energy Calculations
    22nd “Darmstadt” Molecular Modeling Workshop, Erlangen, April 29-30, 2008.
  • Jürgen Wittmann, Frank Beierlein, Harald Lanig, Christof Jäger, Tim Clark and Harald Gröger
    Rational Design of Enzyme Promiscuity by Molecular Model(l)ing: Theoretical Concepts towards non-Natural Biocatalytic Reactions
    Model(l)ing´09 – Annual Molecular Modelling Workshop & Annual International Meeting of the MGMS, Erlangen, Sept 6-11, 2009.
  • Frank Beierlein, Jonathan Essex
    A DFT-QM/MM-Approach to Consider Polarisation in Protein-Ligand Binding Free Energy Calculations
    Model(l)ing´09 – Annual Molecular Modelling Workshop & Annual International Meeting of the MGMS, Erlangen, Sept 6-11, 2009.
  • Frank Beierlein, Jonathan Essex
    A Multiscale Modelling Approach for Free Energies of Complexation
    2nd EAM Symposium, Kloster Banz/Bad Staffelstein, Nov 16-18, 2010.
  • Frank Beierlein, Gül Altinbas Özpinar, Timothy Clark, Wolfgang Peukert
    Urea Nanocrystals: Insights from Atomistic Molecular Dynamics Simulations
    2nd EAM Symposium, Kloster Banz/Bad Staffelstein, Nov 16-18, 2010.
  • Andreas Krause, Frank Beierlein, Christof Jäger, Piotr Fita, Eric Vauthey, Timothy Clark
    Molecular Dynamics Simulations of Multiphase Systems: Dyes as Probes for Local Viscosity at Liquid-Liquid Interfaces
    2nd EAM Symposium, Kloster Banz/Bad Staffelstein, Nov 16-18, 2010.
  • Frank Beierlein, Jonathan Essex
    A Simple QM/MM Approach for Capturing Polarization Effects in Protein-Ligand Binding Free Energy Calculations
    25th Molecular Modeling Workshop, Erlangen, April 4-6, 2011.
  • Frank Beierlein, Gül Altınbaş Özpınar, Wolfgang Peukert, Dirk Zahn, Timothy Clark
    A Test of Improved Force Field Parameters for Urea: Molecular-Dynamics Simulations of Urea Crystals
    3rd EAM Symposium, Oberhof, Nov 7-10, 2011.
  • Frank R. Beierlein, G. Geoff Kneale, Timothy Clark
    Predicting the Effects of Base-Pair Mutations in DNA-Protein Complexes by Thermodynamic Integration
    26th Molecular Modeling Workshop, Erlangen, March 12-14, 2012.
  • Andreas Krause, Frank Beierlein, Christof Jäger, Piotr Fita, Eric Vauthey, Tim Clark
    Molecular Dynamics Simulations of Multiphase Systems: Complementing Experimental SHG Studies
    EAM Summer School 2012, Kloster Banz/Bad Staffelstein, June 28-30, 2012.
  • Frank R. Beierlein, G. Geoff Kneale, Timothy Clark
    Predicting the Effects of Base-Pair Mutations in DNA-Protein Complexes by Thermodynamic Integration
    EAM Summer School 2012, Kloster Banz/Bad Staffelstein, June 28-30, 2012.
  • Andreas Krause, Frank Beierlein, Christof Jäger, Piotr Fita, Eric Vauthey, Tim Clark
    Molecular Dynamics Simulations of Multiphase Systems: Complementing Experimental SHG Studies
    4th EAM Symposium, Oberhof, Oct 22-24, 2012.
  • Frank R. Beierlein, Kathrin Engelhardt, Björn Braunschweig, Wolfgang Peukert, Timothy Clark
    Beta-Lactoglobulin at the Water-Air Interface: MD Simulations on Different Time and Length Scales
    4th EAM Symposium, Oberhof, Oct 22-24, 2012.
  • Frank Beierlein, Kathrin Engelhardt, Björn Braunschweig, Wolfgang Peukert, Timothy Clark
    Beta-Lactoglobulin at the Water-Air Interface: MD Simulations on Different Time and Length Scales
    27th Molecular Modeling Workshop, Erlangen, Feb 25-27, 2013.
  • Frank Beierlein, Kathrin Engelhardt, Björn Braunschweig, Wolfgang Peukert, Timothy Clark
    Beta-Lactoglobulin at the Water-Air Interface: MD Simulations on Different Time and Length Scales
    49th Symposium on Theoretical Chemistry 2013, Erlangen, Sept 22-26, 2013.
  • Andreas M. Krause, Frank Beierlein, Christof Jäger, Piotr Fita, Eric Vauthey, Tim Clark
    Molecular Dynamics Simulations of Liquid Phase Interfaces: Understanding the Structure of the Glycerol/Water-Dodecane System
    5th EAM Symposium, Kloster Banz/Bad Staffelstein, Nov 18-20, 2013.
  • Frank Beierlein, Björn Braunschweig, Kathrin Engelhardt, Johannes Walter, Wolfgang Peukert, Timothy Clark
    Multiscale Simulations of Foam Proteins
    5th EAM Symposium, Kloster Banz/Bad Staffelstein, Nov 18-20, 2013.
  • Frank Beierlein, Björn Braunschweig, Kathrin Engelhardt, Johannes Walter, Wolfgang Peukert, Timothy Clark
    Ion and pH Effects on Foam Protein Aggregation
    28th Molecular Modeling Workshop, Erlangen, Mar 17-19, 2014.
  • Frank Beierlein, Björn Braunschweig, Kathrin Engelhardt, Lena Glas, Wolfgang Peukert, Timothy Clark
    The Effects of Alkali Ions on the Aggregation and Interfacial Adsorption of beta-Lactoglobulin
    29th Molecular Modeling Workshop, Erlangen, Mar 9-11, 2015.
  • Frank Beierlein, Miguel Paradas Palomo, Dmitry I. Sharapa, Oleksii Zozulia, Andriy Mokhir, Timothy Clark
    DNA-Dye-Conjugates: Conformations and Spectra of Fluorescence Probes
    30th Molecular Modeling Workshop, Erlangen, Apr 4-6, 2016.
  • Frank Beierlein, Miguel Paradas Palomo, Dmitry I. Sharapa, Oleksii Zozulia, Andriy Mokhir, Timothy Clark
    DNA-Dye-Conjugates for Detecting Nucleic Acids in Live Cells
    31st Molecular Modeling Workshop, Erlangen, Mar 27-29, 2017.
  • Amir H. Hakimioun, Frank R. Beierlein, Dmitry I. Sharapa, Andriy Mokhir, Timothy Clark
    Enzyme-Independent Chemical Reactions for Chemistry in Living Cells
    31st Molecular Modeling Workshop, Erlangen, Mar 27-29, 2017.