Dr. Frank Beierlein: Publications, Talks and Posters
Maria Handke, Frank Beierlein, Petra Imhof, Matthias Schiedel, Simon Hammann
New fluorogenic triacylglycerols as sensors for dynamic measurement of lipid oxidation
Analytical and Bioanalytical Chemistry 2024, accepted.
Publications from FAU Current Research Information System (CRIS)
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)
S. Daum, J. Toms, V. Reshetnikov, H. G. Özkan, F. Hampel, S. Maschauer, A. Hakimioun, F. Beierlein, L. Sellner, M. Schmitt, O. Prante, A. Mokhir
Identification of Boronic Acid Derivatives as an Active Form of N-Alkylaminoferrocene-Based Anticancer Prodrugs and Their Radiolabeling with 18F
Bioconjugate Chem. 2019, 30, 1077-1086. (DOI: 10.1021/acs.bioconjchem.9b00019)
O. Zozulia, T. Bachmann, N. Deussner-Helfmann, F. Beierlein, M. Heilemann, A. Mokhir
Red light-triggered nucleic acid-templated reaction based on cyclic oligonucleotide substrates
Chem. Commun. 2019, 55, 10713-10716. (DOI: 10.1039/C9CC03587G)
S. Chercheja, S. Daum, H.-G. Xu, F. R. Beierlein, A. Mokhir
Hybrids of a 9-anthracenyl moiety and fluorescein as chemodosimeters for detection of singlet oxygen in live cells
Org. Biomol. Chem. 2019, 17, 9883-9891. (DOI: 10.1039/C9OB02070E).
M. Kriebel, M. Hennemann, F. R. Beierlein, D. D. Medina, T. Bein, T. Clark
Propagation of Holes and Electrons in Metal-Organic Frameworks
J. Chem. Inf. Model. 2019, 59, 5057-5064. (DOI: 10.1021/acs.jcim.9b00461)
J. S. Hardwick, M. M. Haugland, A. H. El-Sagheer, D. Ptchelkine, F. R. Beierlein, A. N. Lane, T. Brown, J. E. Lovett, E. A. Anderson
2′-Alkynyl spin-labelling is a minimally perturbing tool for DNA structural analysis
Nucleic Acids Res. 2020, 48, 2830-2840. (DOI: 10.1093/nar/gkaa086)
L. Eberlein, F. R. Beierlein, N. J. R. van Eikema Hommes, A. Radadiya, J. Heil, S. A. Benner, T. Clark, S. M. Kast, N. G. J. Richards
Tautomeric Equilibria of Nucleobases in the Hachimoji Expanded Genetic Alphabet
J. Chem. Theory Comput. 2020, 16, 2766-2777. (DOI: 10.1021/acs.jctc.9b01079)
S. Volkenandt, F. Beierlein, P. Imhof
(S. Volkenandt and F. Beierlein contributed equally)
Interaction of Thymine DNA Glycosylase with Oxidised 5-Methyl-Cytosines in their Amino- and Imino-Forms
Molecules 2021, 26, 5728. (DOI: 10.3390/molecules26195728)
Frank Beierlein, Senta Volkenandt, Petra Imhof
Oxidation Enhances Binding of Extra-Helical 5-Methyl-Cytosines by Thymine DNA Glycosylase
J. Phys. Chem. B 2022, 126, 6, 1188-1201. (DOI: 10.1021/acs.jpcb.1c09896)
I. Klemt, V. Reshetnikov, S. Dutta, G. Bila, R. Bilyy, I. C. Cuartero, A. Hidalgo, A. Wünsche, M. Böhm, M. Wondrak, L. A. Kunz-Schughart, R. Tietze, F. Beierlein, P. Imhof, S. Gensberger-Reigl, M. Pischetsrieder, M. Körber, T. Jost, A. Mokhir
A concept of dual-responsive prodrugs based on oligomerization-controlled reactivity of ester groups: an improvement of cancer cells versus neutrophils selectivity of camptothecin
RSC Med. Chem. 2024, 15, 1189-1197. (DOI: 10.1039/D3MD00609C)
Frank Beierlein, Anselm H. C. Horn, Heinrich Sticht, Andriy Mokhir, Petra Imhof
In Silico Study of Binding of Camptothecin-Based Pro-Drugs to Human Carboxylesterase 2
Biomolecules 2024, 14, 153. (DOI: 10.3390/biom14020153)
Maria Handke, Frank Beierlein, Petra Imhof, Matthias Schiedel, Simon Hammann
New fluorogenic triacylglycerols as sensors for dynamic measurement of lipid oxidation
Analytical and Bioanalytical Chemistry 2024, accepted.
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.
Computer-Chemie-Centrum/AK Clark
Tetracyclinresistenzen – eine Herausforderung für Simulation und Experiment
Lange Nacht der Wissenschaften, Erlangen, 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.
Frank Beierlein
(Computational) Chemistry in Live Cells
EFI Symposium 2018, Erlangen, May 10, 2018.
Frank Beierlein, Senta Volkenandt, Petra Imhof
DNA-Repair Mechanisms: Molecular Simulations and Computational Alchemy
35th Molecular Modeling Workshop, Erlangen, Mar 13-15, 2023.
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.
Frank R. Beierlein, Janet E. Lovett, Edward A. Anderson
Spin-Labelled DNA Oligomers: Simulation and Experiment
32nd Molecular Modeling Workshop, Erlangen, Mar 12-14, 2018.
Amir H. Hakimioun, Frank R. Beierlein, Andriy Mokhir, Timothy Clark
Enzyme-Independent Chemical Reactions for Chemistry in Living Cells
32nd Molecular Modeling Workshop, Erlangen, Mar 12-14, 2018.
Frank R. Beierlein, Jack S. Hardwick, Marius M. Haugland, Afaf H. El-Sagheer, Denis Ptchelkine, Tom Brown, Janet E. Lovett, Edward A. Anderson
A Multi-Technique Approach to DNA Structure Determination
33rd Molecular Modeling Workshop, Erlangen, Apr 08-10, 2019.
Frank R. Beierlein, Jack S. Hardwick, Marius M. Haugland, Afaf H. El-Sagheer, Denis Ptchelkine, Andrew N. Lane, Tom Brown, Janet E. Lovett, Edward A. Anderson
Probing DNA Conformation: A Multi-Technique Approach
34th Molecular Modeling Workshop, Erlangen, Feb 17-19, 2020.
NHR@FAU, Computer-Chemie-Centrum/AK Imhof
DNA-Reparatur im Supercomputer
Lange Nacht der Wissenschaften, Erlangen, May 21, 2022
Frank Beierlein, Senta Volkenandt, Petra Imhof
DNA-Repair Mechanisms: Molecular Simulations and Computational Alchemy
35th Molecular Modeling Workshop, Erlangen, Mar 13-15, 2023.
Jorge Antonio Amador-Balderas, Frank Beierlein Senta Volkenandt, Petra Imhof
Effect of N140D and T197A mutations on DNA repair enzyme Thymine DNA Glycosylase
35th Molecular Modeling Workshop, Erlangen, Mar 13-15, 2023.
Frank Beierlein, Senta Volkenandt, Petra Imhof
DNA-Repair Mechanisms: Molecular Simulations and Computational Alchemy
Hybrid Workshop on Computer Simulation and Theory of Macromolecules, Hünfeld, April 28-29, 2023.
Frank Beierlein, Senta Volkenandt, Petra Imhof
DNA-Repair Mechanisms: Molecular Simulations and Computational Alchemy
NHR Conference ’23, Berlin, Sept 18-20, 2023.
NHR@FAU, Computer-Chemie-Centrum/AK Imhof
DNA-Reparatur im Supercomputer
Lange Nacht der Wissenschaften, Erlangen, Oct 21, 2023.
Jorge Antonio Amador Balderas, Frank Beierlein, Petra Imhof
Insight into the active site conformation of DNA repair Enzyme MBD4 from molecular
simulations
36th Molecular Modeling Workshop, Erlangen, Mar 4-6, 2024.
Frank Beierlein, Anselm H. C. Horn, Heinrich Sticht, Andriy Mokhir, Petra Imhof
In Silico Study of Binding of Camptothecin-Based Pro-Drugs to Human Carboxylesterase 2
36th Molecular Modeling Workshop, Erlangen, Mar 4-6, 2024.
