Pharmazeutische Chemie

Publication List - Thomas E. Exner

Publications

  1. A Biophysical Study with Carbohydrate Derivatives Explains the Molecular Basis of Monosaccharide Selectivity of the Pseudomonas aeruginosa Lectin LecB.
    Sommer R., Exner T. E., Titz A.
    PLOSone 9 (11) 1-22 (2014)
  2. Performance of Protein-Ligand Docking with Simulated Chemical Shift Perturbations
    ten Brink, T.; Aguirre, C.; Exner, T. E.; Krimm, I.
    J.Chem.Inf.Model.(ASAP)
  3. Toward the Quantum Chemical Calculation of NMR Chemical Shifts of Proteins 3. Conformational Sampling and Explicit Solvents model
    Exner, T. E.; Frank, A.; Onila, I.; Möller, H. M.
    J.Chem.Theory Comput. 8, 4818-4827 (2012)
  4. Are predefined decoy sets of ligand poses able to quantify scoring function accuracy?
    Korb, O.; ten Brink, T.; Fredrick Robin Devados V.; Keil, M.; Exner, T. E.
    J.Comput.Aided Mol.Des. 26, 185-197 (2012).
  5. Toward the Quantum Chemical Calculation of NMR Chemical Shifts of Proteins 2: Level of Theory, Basis Set, and Solvents Model Dependence
    Frank, A.; Möller, H.; Exner, T. E.
    J.Chem.Theory Comput. 8, 1480-1492 (2012)
  6. Interaction structure of the complex between neuroprotective factor humanin and Alzheimer's ß-amyloid peptide revealed by affinity-mass spectrometry and molecular modeling
    Maftei, M.; Tian, X.; Manea, M.; Exner, T. E.; Schwanzar, D.; von Arnim, C.; Przybylski, M.
    J.Pept.Sci. 18, 373-382 (2012)
  7. Synthesis and Photoswitching Studies of Difurylperfluorocyclopentenes with Extended p-Systems
    Sysoiev, D.; Fedoseev, A.; Kim, Y.; Exner, T. E.; Boneberg, J.; Huhn, T.; Leiderer, P.; Scheer, E.; Groth, U.; Steiner, U. E.
    Chemistry 17, 6663-6672 (2011)
  8. Critical Investigation on the Pseudobond Approach for QM/MM and Fragment-Based QM methods
    Exner, T. E.
    Int.J.Quantum Chem. 111, 1002-1012 (2011)
  9. Towards the Quantum Chemical Calculation of NMR Chemical Shifts of Proteins
    Frank, A.; Onila, I.; Möller, H.; Exner, T. E.
    Proteins 79, 2189-2202 (2011)
  10. Accelerating Molecular Docking Calculations Using Graphics Processing Units
    Korb, O.; Stützle, T.; Exner, T. E.
    J.Chem.Inf.Model. 51, 865-887 (2011)
  11. Structures of DNA polymerases caught processing size-augmented nucleotide probes
    Betz, K.; Streckenbach, F.; Schnur, A.; Exner, T. E.; Welte, W.; Diederichs, K.; Marx, A.
    Angew.Chem.Int.Ed. 49, 5181-5184 (2010)
  12. pKa Based Protonation States and Microspecies for Protein-Ligand Docking
    ten Brink, T.; Exner, T. E.
    J.Comput.Aided Mol.Des. 24, 935-942 (2010)
  13. A short note on the analysis of distance measurements by electron paramagnetic resonance
    Domingo Köhler, S.; Spitzbarth, M.; Diederichs, K.; Exner, T. E.; Drescher, M.
    J.Magn.Res. 208, 167-170 (2010)
  14. NMR-guided Molecular Docking of a Protein-Peptide Complex Based on Ant Colony Optimization
    Korb, O.; Möller, H.; Exner, T. E.
    ChemMedChem 5, 1001-1006 (2010)
  15. pharmACOphore: Multiple Flexible Ligand Alignment Based on Ant Colony Optimization
    Korb, O.; Monecke, P.; Hessler, G.; Stützle, T.; Exner, T. E.
    J.Chem.Inf.Model. DOI: 10.1021/ci1000218, (2010)
  16. Improving the Interaction of Myc-Interfering Peptides with Myc using Molecular Dynamics Simulations
    Jouaux, E. M.; Timm, B. B.; Arndt, K. M.; Exner, T. E.
    J.Pept.Sci. 15, 5-15 (2009)
  17. Molecular Visualization in the Rational Drug Design Process
    Keil, M.; Marhöfer, R. J.; Rohwer, A.; Selzer, P. M.; Brickmann, J.; Korb, O.; Exner, T. E.
    Frontiers in Bioscience 14, 2559-2583 (2009)
  18. Improvements for the Generalized Hybrid Orbital Method
    Eckard, S.; Exner, T. E.
    Int.J.Quantum Chem. 109, 1451-1463 (2009)
  19. The Influence of Protonation States on Protein-Ligand Docking Results
    ten Brink, T.; Exner, T. E. "
    J.Chem.Inf.Model. 49, 1535-1546 (2009)
  20. Insights into the High Fidelity of a DNA Polymerase I Mutant
    Exner, T. E.
    J.Mol.Model. 15, 1271-1280 (2009)
  21. Scouting Novel Protein Kinase A (PKA) Inhibitors by Using a Consensus Docking Based Virtual Screening Approach
    Zonta, N.; Cozza, G.; Gianoncelli, A.; Korb, O.; Exner, T. E.; Meggio, F.; Zagotto, G.; Moro, S.
    Lett.Drug Des.Decov. 6, 327-336 (2009)
  22. Human Telomeric Quadruplex Conformations Studied by EPR-PELDOR
    Singh, V.; Azarkh, M.; Exner, T. E.; Hartig, J. S.; Drescher, M.
    Angew.Chem.Int.Ed. 48, 9728-9730 (2009)
  23. Parametrization of an Empricical Model for the Prediction of n-Octanol, Alkane and Cyclohexane / Water as well as Brain / Blood Partition Coefficients
    Zerara, M.; Brickmann, J.; Kretschmer, R.; Exner, T. E.
    J.Comput.Aided Mol.Des. 23, 105-111 (2009)
  24. Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS
    Korb, O.; Stützle, T.; Exner, T. E.
    J.Chem.Inf.Model. 49, 84-96 (2009)
  25. An ant colony optimization approach to flexible protein-ligand docking
    Korb, O.; Stützle, T.; Exner, T. E.
    Swarm Intell. 1, 115-134 (2007)
  26. PLANTS: Application of Ant Colony Optimization to Structure-Based Drug Design
    Korb, O.; Stützle, T.; Exner, T. E.
    Lecture Notes in Computer Science 4150, 247-258 (2006)
  27. Hybrid Particle Swarm Optimization: An Examination of the Influence of Iterated Improvement Algorithms on the Optimization Behaviour
    Gimmler, J.; Stützle, T.; Exner, T. E.
    Lecture Notes in Computer Science 4150, 436-443 (2006)
  28. Structural Changes and Binding Characteristics of the Tetracycline-Repressor Binding Site on Induction
    Lanig, H.; Othersen, O. G.; Seidel, U.; Beierlein, F. R.; Exner, T. E.; Clark, T.
    J.Med.Chem. 49, 3444-3447 (2006)
  29. Generalized Hybrid Orbitals in the FA-ADMA Method
    Eckard, S.; Exner, T. E.
    Z.Phys.Chem. 220, 927-944 (2006)
  30. Fuzzy Fragment Selection Strategies, Basis Set Dependence, and HF - DFT Comparisons in the Applications of the ADMA Method of Macromolecular Quantum Chemistry
    Szekeres, Z.; Exner, T. E.; Mezey, P. G.
    Int.J.Quantum Chem. 104, 847-860 (2005)
  31. Evaluation of the Field-Adapted ADMA Approach: Absolute and Relative Energies of Crambin
    Exner, T. E.; Mezey, P. G.
    Phys.Chem.Chem.Phys. 7, 4061-4069 (2005)
  32. The Field-Adapted ADMA Approach: Introducing Point Charges
    Exner, T. E.; Mezey, P. G.
    J.Phys.Chem.A 108, 4301-4309 (2004)
  33. Pattern Recognition Strategies for Molecular Surfaces III. Binding Site Prediction with a Neural Network
    Keil, M.; Exner, T. E.; Brickmann, J.
    J.Comp.Chem. 25, 779-789 (2003)
  34. Ab Initio Quality Properties for Macromolecules Using the ADMA Approach
    Exner, T. E.; Mezey, P. G.
    J.Comp.Chem. 24, 1980-1986 (2003)
  35. New Fuzzy Logic Strategies for Bio-molecular Recognition
    Exner, T. E.; Keil, M.; Brickmann, J.
    SAR QSAR Environ.Res. 14, 421-431 (2003)
  36. Comparison of Nonlinear Transformation Methods for Electron Density Approximation
    Exner, T. E.; Mezey, P. G.
    J.Phys.Chem.A 106, 5504-5509 (2002).
  37. Pattern Recognition Strategies for Molecular Surfaces I. Pattern Generation Using Fuzzy Set Theory
    Exner, T. E.; Keil, M.; Brickmann, J.
    J.Comp.Chem. 23, 1176-1187 (2002)
  38. Pattern Recognition Strategies for Molecular Surfaces II. Surface Complementarity
    Exner, T. E.; Keil, M.; Brickmann, J.
    J.Comp.Chem. 23, 1188-1197 (2002)
  39. Ab Initio Quality Electrostatic Potentials for Proteins: An Application of the ADMA Approach
    Exner, T. E.; Mezey, P. G.
    J.Phys.Chem.A 106, 11791-11800 (2002)
  40. The Identification of Complementarity of Molecular Surfaces Using Fuzzy Set Theory
    Exner, T. E.; Brickmann, J.
    J.Mol.Model. 7, 370-373 (2001)
  41. Molecular Graphics: Trends and Perspectives
    Brickmann, J.; Keil, M.; Exner, T. E.; Marhöfer, R.
    J.Mol.Model. 6, 328-340 (2000)
  42. Identification of Substrate Channels and Protein Cavities
    Exner, T. E.; Keil, M.; Moeckel, G.; Brickmann, J.
    J.Mol.Model. 4, 340-343 (1998)
  43. Molecular Shape Recognition Using Fuzzy Logic Strategies
    Exner, T. E.; Brickmann, J.
    Match - Communications in Mathematical and in Computer Chemistry 38, 53-80 (1998)
  44. Fuzzy Logic Strategien zur Behandlung der Molekularen Erkennung
    Exner, T. E.; Brickmann, J.
    GIT Labor-Fachzeitschrift 11, 1144-1146 (1998)
  45. Characterisation of Protein-Ligand Interfaces: Separating Surface
    Keil, M.; Exner, T. E.; Brickmann, J.
    J.Mol.Model. 4, 335-339 (1998)
  46. New docking algorithm based on fuzzy set theory
    Exner, T. E.; Brickmann, J.
    J.Mol.Model. 3, 321-324 (1997)

Books and Book Chapters

  1. Approximations of Long-Range Interactions in Fragment-Based Quantum Chemical Approaches
    Eckard, S.; Frank, A.; Onila, I.; Exner, T. E.
    in Linear-Scaling Techniques in Quantum Chemistry: Methods and Applications; Zalesny, R., Leszczynski, J., Papadopoulos, M., Mezey, P. G. (Eds.); Springer: 2011; pp 157-173.
  2. Comparison of the Incorporation of Watson-Crick Complementary and Mismatched Nucleotides Catalyzed by DNA Polymerase I
    Exner, T. E.
    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
  3. Fuzzy Set Theory and Fuzzy Logic and Its Application to Molecular Recognition
    Exner, T. E.; Keil, M.; Brickmann, J.
    in Chemoinformatics - From Data to Knowledge; Gasteiger, J., Engel, T. (Eds.); Wiley-VCH: Weinheim, 2003; pp 1216-1238
  4. Computer Visualization - Tools for the Man-Machine-Communication in Molecular Science
    Keil, M.; Borosch, T.; Exner, T. E.; Brickmann, J.
    in Chemoinformatics - From Data to Knowledge; Gasteiger, J., Engel, T. (Eds.); Wiley-VCH: Weinheim, 2003; pp 320-343.
  5. Fuzzy Logic Strategies for the Treatment of the Molecular Recognition Problem
    Exner, T. E.; Keil, M.; Brickmann, J.
    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
  6. Molecular Models: Visualization
    Brickmann, J.; Keil, M.; Exner, T. E.; Marhöfer, R.; Moeckel, G.
    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.

Conference Proceedings

  1. Guiding protein-ligand docking with different experimental NMR-data
    ten Brink, T., Onila, I., Mazur, A., Korb, O., Möller, H., Greisinger, C., Carlomagno, T., and Exner, T. E.
    J.Cheminform. 4 (Suppl. I),P39 (2012)
  2. pharmACOphore: multiple flexible ligand alignment based on ant colony optimization
    Hessler, G., Korb, O., Monecke, P., Stützle, T., and Exner, T. E.
    J.Cheminform. 2 (Suppl. I),P17 (2010)
  3. A combined combinatorial and pKa-based approach to ligand protonation states
    ten Brink, T. and Exner, T. E.
    J.Cheminform. 2 (Suppl. I),P43 (2010)
  4. Protein Structure Calculation wit a Min-Max Ant System
    Gimmler, J., Gronwald, W., Möller, H., and Exner, T. E.
    Chem.Central J. 3 (Suppl I),P52 (2009)
  5. New and Improved Features of the Docking Software PLANTS
    Exner, T. E., Korb, O., and ten Brink, T.
    Chem.Central J. 3 (Suppl I),P16 (2009)
  6. Ligand Protonation States and Stereoisomers in Virtual Screening
    ten Brink, T. and Exner, T. E.
    Chem.Central J. 3 (Suppl I),P14 (2009)
  7. Multi-body interactions in molecular docking: treatment of water molecules and multiple ligands
    Korb, O., Stützle, T., and Exner, T. E.
    Chem.Central J. 2 (Suppl I),P5 (2008)
  8. The influence of protonation in protein-ligand docking
    ten Brink, T. and Exner, T. E.
    Chem.Central J. 2 (Suppl I),P12 (2008)
  9. Parametrization of the molecular free energy surface density (MolFESD) for different solvents and brain-blood barrier partitioning
    Zerara, M., Kretschmer, R., Exner, T. E., and Brickmann, J.
    Chem.Central J. 2 (Suppl I),P20 (2008)
  10. Prediction and classification of protein binding sites
    Keil, M., Exner, T. E., and Brickmann, J.
    in Abstracts of Papers; 226th ACS National Meeting, New York, NY, United States, September 7-11, 2003, (2003)
  11. Recognition Using Fuzzy Logic Strategies
    Brickmann, J. and Exner, T. E.
    in Chemistry Forum '99, Proceedings of the Vth International Symposium Warschau,15-23 (1999)
  12. Molecular Modeling Information Transfer with VRML: From Small Molecules to Large Systems in Bioscience
    Moeckel, G., Keil, M., Exner, T. E., and Brickmann, J.
    in Proceedings of the Pacific Symposium on Biocomputing '98,327-338 (1998)
  13. Molecular Modelling on the Internet: Examples and Perspectives
    Brickmann, J., Moeckel, G., Exner, T. E., and Keil, M.
    in Proceedings of the 1997 Chemical Information Conference,107-120 (1997).