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- LIST OF
PUBLICATIONS
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Dr. Thomas E. Exner
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Publications
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1)
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Exner, T. E. "Critical Investigation on the Pseudobond Approach for QM/MM and Fragment-Based QM methods" Int.J.Quantum Chem. 111, 1002-1012 (2011).
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2)
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Frank, A.; Onila, I.; Möller, H.; Exner, T. E. "Towards the Quantum Chemical Calculation of NMR Chemical Shifts of Proteins" Proteins 79, 2189-2202 (2011).
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3)
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Korb, O.; Stützle, T.; Exner, T. E. "Accelerating Molecular Docking Calculations Using Graphics Processing Units" J.Chem.Inf.Model. 51, 865-887 (2011).
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4)
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Sysoiev, D.; Fedoseev, A.; Kim, Y.; Exmer, T. E.; Boneberg, J.; Huhn, T.; Leiderer, P.; Scheer, E.; Groth, U.; Steiner, U. E. "Synthesis and Photoswitching Studies of Difurylperfluorocyclopentenes with Extended p-Systems" Chemistry 17, 6663-6672 (2011).
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5)
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Domingo Köhler, S.; Spitzbarth, M.; Diederichs, K.; Exner, T. E.; Drescher, M. "A short note on the analysis of distance measurements by electron paramagnetic resonance" J.Magn.Res. 208, 167-170 (2010).
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6)
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Korb, O.; Möller, H.; Exner, T. E. "NMR-guided Molecular Docking of a Protein-Peptide Complex Based on Ant Colony Optimization" ChemMedChem 5, 1001-1006 (2010).
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7)
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Korb, O.; Monecke, P.; Hessler, G.; Stützle, T.; Exner, T. E. "pharmACOphore: Multiple Flexible Ligand Alignment Based on Ant Colony Optimization" J.Chem.Inf.Model. DOI: 10.1021/ci1000218, (2010).
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8)
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Betz, K.; Streckenbach, F.; Schnur, A.; Exner, T. E.; Welte, W.; Diederichs, K.; Marx, A. "Structures of DNA polymerases caught processing size-augmented nucleotide probes" Angew.Chem.Int.Ed. 49, 5181-5184 (2010).
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9)
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ten Brink, T.; Exner, T. E. "pKa Based Protonation States and Microspecies for Protein-Ligand Docking" J.Comput.Aided Mol.Des. 24, 935-942 (2010).
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10)
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Singh, V.; Azarkh, M.; Exner, T. E.; Hartig, J. S.; Drescher, M. "Human Telomeric Quadruplex Conformations Studied by EPR-PELDOR" Angew.Chem.Int.Ed. 48, 9728-9730 (2009).
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11)
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Zerara, M.; Brickmann, J.; Kretschmer, R.; Exner, T. E. "Parametrization of an Empricical Model for the Prediction of n-Octanol, Alkane and Cyclohexane / Water as well as Brain / Blood Partition Coefficients" J.Comput.Aided Mol.Des. 23, 105-111 (2009).
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12)
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Korb, O.; Stützle, T.; Exner, T. E. "Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS" J.Chem.Inf.Model. 49, 84-96 (2009).
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13)
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Jouaux, E. M.; Timm, B. B.; Arndt, K. M.; Exner, T. E. "Improving the Interaction of Myc-Interfering Peptides with Myc using Molecular Dynamics Simulations" J.Pept.Sci. 15, 5-15 (2009).
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14)
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Keil, M.; Marhöfer, R. J.; Rohwer, A.; Selzer, P. M.; Brickmann, J.; Korb, O.; Exner, T. E. "Molecular Visualization in the Rational Drug Design Process" Frontiers in Bioscience 14, 2559-2583 (2009).
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15)
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Eckard, S.; Exner, T. E. "Improvements for the Generalized Hybrid Orbital Method" Int.J.Quantum Chem. 109, 1451-1463 (2009).
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16)
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ten Brink, T.; Exner, T. E. "The Influence of Protonation States on Protein-Ligand Docking Results" J.Chem.Inf.Model. 49, 1535-1546 (2009).
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17)
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Exner, T. E. "Insights into the High Fidelity of a DNA Polymerase I Mutant" J.Mol.Model. 15, 1271-1280 (2009).
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18)
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Zonta, N.; Cozza, G.; Gianoncelli, A.; Korb, O.; Exner, T. E.; Meggio, F.; Zagotto, G.; Moro, S. "Scouting Novel Protein Kinase A (PKA) Inhibitors by Using a Consensus Docking Based Virtual Screening Approach" Lett.Drug Des.Decov. 6, 327-336 (2009).
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19)
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Korb, O.; Stützle, T.; Exner, T. E. "An ant colony optimization approach to flexible protein-ligand docking" Swarm Intell. 1, 115-134 (2007).
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20)
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Gimmler, J.; Stützle, T.; Exner, T. E. "Hybrid Particle Swarm Optimization: An Examination of the Influence of Iterated Improvement Algorithms on the Optimization Behaviour" Lecture Notes in Computer Science 4150, 436-443 (2006).
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21)
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Lanig, H.; Othersen, O. G.; Seidel, U.; Beierlein, F. R.; Exner, T. E.; Clark, T. "Structural Changes and Binding Characteristics of the Tetracycline-Repressor Binding Site on Induction" J.Med.Chem. 49, 3444-3447 (2006).
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22)
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Eckard, S.; Exner, T. E. "Generalized Hybrid Orbitals in the FA-ADMA Method" Z.Phys.Chem. 220, 927-944 (2006).
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23)
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Korb, O.; Stützle, T.; Exner, T. E. "PLANTS: Application of Ant Colony Optimization to Structure-Based Drug Design" Lecture Notes in Computer Science 4150, 247-258 (2006).
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24)
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Exner, T. E.; Mezey, P. G. "Evaluation of the Field-Adapted ADMA Approach: Absolute and Relative Energies of Crambin" Phys.Chem.Chem.Phys. 7, 4061-4069 (2005).
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25)
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Szekeres, Z.; Exner, T. E.; Mezey, P. G. "Fuzzy Fragment Selection Strategies, Basis Set Dependence, and HF - DFT Comparisons in the Applications of the ADMA Method of Macromolecular Quantum Chemistry" Int.J.Quantum Chem. 104, 847-860 (2005).
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26)
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Exner, T. E.; Mezey, P. G. "The Field-Adapted ADMA Approach: Introducing Point Charges" J.Phys.Chem.A 108, 4301-4309 (2004).
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27)
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Keil, M.; Exner, T. E.; Brickmann, J. "Pattern Recognition Strategies for Molecular Surfaces III. Binding Site Prediction with a Neural Network" J.Comp.Chem. 25, 779-789 (2003).
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28)
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Exner, T. E.; Mezey, P. G. "Ab Initio Quality Properties for Macromolecules Using the ADMA Approach" J.Comp.Chem. 24, 1980-1986 (2003).
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29)
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Exner, T. E.; Keil, M.; Brickmann, J. "New Fuzzy Logic Strategies for Bio-molecular Recognition" SAR QSAR Environ.Res. 14, 421-431 (2003).
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30)
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Exner, T. E.; Keil, M.; Brickmann, J. "Pattern Recognition Strategies for Molecular Surfaces I. Pattern Generation Using Fuzzy Set Theory" J.Comp.Chem. 23, 1176-1187 (2002).
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31)
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Exner, T. E.; Keil, M.; Brickmann, J. "Pattern Recognition Strategies for Molecular Surfaces II. Surface Complementarity" J.Comp.Chem. 23, 1188-1197 (2002).
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32)
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Exner, T. E.; Mezey, P. G. "Ab Initio Quality Electrostatic Potentials for Proteins: An Application of the ADMA Approach" J.Phys.Chem.A 106, 11791-11800 (2002).
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33)
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Exner, T. E.; Mezey, P. G. "Comparison of Nonlinear Transformation Methods for Electron Density Approximation" J.Phys.Chem.A 106, 5504-5509 (2002).
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34)
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Exner, T. E.; Brickmann, J. "The Identification of Complementarity of Molecular Surfaces Using Fuzzy Set Theory" J.Mol.Model. 7, 370-373 (2001).
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35)
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Brickmann, J.; Keil, M.; Exner, T. E.; Marhöfer, R. "Molecular Graphics: Trends and Perspectives" J.Mol.Model. 6, 328-340 (2000).
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36)
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Exner, T. E.; Brickmann, J. "Molecular Shape Recognition Using Fuzzy Logic Strategies" Match - Communications in Mathematical and in Computer Chemistry 38, 53-80 (1998).
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37)
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Exner, T. E.; Brickmann, J. "Fuzzy Logic Strategien zur Behandlung der Molekularen Erkennung" GIT Labor-Fachzeitschrift 11, 1144-1146 (1998).
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38)
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Keil, M.; Exner, T. E.; Brickmann, J. "Characterisation of Protein-Ligand Interfaces: Separating Surface" J.Mol.Model. 4, 335-339 (1998).
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39)
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Exner, T. E.; Keil, M.; Moeckel, G.; Brickmann, J. "Identification of Substrate Channels and Protein Cavities" J.Mol.Model. 4, 340-343 (1998).
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40)
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Exner, T. E.; Brickmann, J. "New docking algorithm based on fuzzy set theory" J.Mol.Model. 3, 321-324 (1997).
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Books and Book Chapters
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1)
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Eckard, S.; Frank, A.; Onila, I.; Exner, T. E. "Approximations of Long-Range Interactions in Fragment-Based Quantum Chemical Approaches" in Linear-Scaling Techniques in Quantum Chemistry: Methods and Applications; Zalesny, R., Leszczynski, J., Papadopoulos, M., Mezey, P. G. (Eds.); Springer: 2011.
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2)
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Exner, T. E. "Comparison of the Incorporation of Watson-Crick Complementary and Mismatched Nucleotides Catalyzed by DNA Polymerase I" in High Performance Computing in Science and Engineering ' 07, Transactions of the High Performance Computing Center, Stuttgart (HLRS) 2007; Nagel, W. E., Kröner, D. B., Resch, M. (Eds.); Springer: Berlin, 2007.
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3)
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Exner, T. E.; Keil, M.; Brickmann, J. "Fuzzy Set Theory and Fuzzy Logic and Its Application to Molecular Recognition" in Chemoinformatics - From Data to Knowledge; Gasteiger, J., Engel, T. (Eds.); Wiley-VCH: Weinheim, 2003; pp 1216-1238.
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4)
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Keil, M.; Borosch, T.; Exner, T. E.; Brickmann, J. "Computer Visualization - Tools for the Man-Machine-Communication in Molecular Science –" in Chemoinformatics - From Data to Knowledge; Gasteiger, J., Engel, T. (Eds.); Wiley-VCH: Weinheim, 2003; pp 320-343.
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5)
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Exner, T. E.; Keil, M.; Brickmann, J. "Fuzzy Logic Strategies for the Treatment of the Molecular Recognition Problem" in Reviews in Modern Quantum Chemistry: A Celebration of the Contributions of Robert Parr; Sen, K. D. (Ed.); World Scientific Publ.: Singapore, 2002; pp 1735-1766.
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6)
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Brickmann, J.; Keil, M.; Exner, T. E.; Marhöfer, R.; Moeckel, G. "Molecular Models: Visualization" in The Encyclopedia of Computational Chemistry; Schleyer, P. v. R., Allinger, N. C., Clark, T., Gasteiger, J., Kollmann, P. A., Schaefer III, H. F., Schreiner, P. R. (Eds.); John Wiley & Sons: Chichester, 1998; pp 1679-1693.
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Conference Proceedings
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1)
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Gimmler, J., Gronwald, W., Möller, H., and Exner, T. E. "Protein Structure Calculation wit a Min-Max Ant System" Chem.Central J. 3 (Suppl I),P52 (2009).
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2)
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Exner, T. E., Korb, O., and ten Brink, T. "New and Improved Features of the Docking Software PLANTS" Chem.Central J. 3 (Suppl I),P16 (2009).
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3)
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ten Brink, T. and Exner, T. E. "Ligand Protonation States and Stereoisomers in Virtual Screening" Chem.Central J. 3 (Suppl I),P14 (2009).
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4)
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Korb, O., Stützle, T., and Exner, T. E. "Multi-body interactions in molecular docking: treatment of water molecules and multiple ligands" Chem.Central J. 2 (Suppl I),P5 (2008).
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5)
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ten Brink, T. and Exner, T. E. "The influence of protonation in protein-ligand docking" Chem.Central J. 2 (Suppl I),P12 (2008).
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6)
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Zerara, M., Kretschmer, R., Exner, T. E., and Brickmann, J. "Parametrization of the molecular free energy surface density (MolFESD) for different solvents and brain-blood barrier partitioning" Chem.Central J. 2 (Suppl I),P20 (2008).
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7)
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Keil, M., Exner, T. E., and Brickmann, J. "Prediction and classification of protein binding sites" in Abstracts of Papers; 226th ACS National Meeting, New York, NY, United States, September 7-11, 2003, (2003).
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8)
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Brickmann, J. and Exner, T. E. "Recognition Using Fuzzy Logic Strategies" in Chemistry Forum '99, Proceedings of the Vth International Symposium Warschau,15-23 (1999).
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9)
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Moeckel, G., Keil, M., Exner, T. E., and Brickmann, J. "Molecular Modeling Information Transfer with VRML: From Small Molecules to Large Systems in Bioscience" in Proceedings of the Pacific Symposium on Biocomputing '98,327-338 (1998).
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10)
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Brickmann, J., Moeckel, G., Exner, T. E., and Keil, M. "Molecular Modelling on the Internet: Examples and Perspectives" in Proceedings of the 1997 Chemical Information Conference,107-120 (1997).
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