Curriculum Vitae - Dr. Thomas E. Exner - Universität Konstanz

Curriculum Vitae
Dr. Thomas E. Exner, Fachbereich Chemie, Universität Konstanz, 78457 Konstanz
Curriculum Vitae
Dr.-Ing. Dipl.-Ing. Thomas Eckart Exner
Address
Fachbereich Chemie
und Zukunftskolleg
Universität Konstanz
78457 Konstanz
Germany
Tel: +49-(0)7531-882015
Fax: +49-(0)7531-883587
E-Mail: thomas.exner@chemie.uni-konstanz.de
Web: http://www.tcd.uni-konstanz.de/
DATE OF BIRTH: 26. Juni 1972
PLACE OF BIRTH: Stuttgart
NATIONALITY: Austrian
MARITAL STATUS: Married, three children
EDUCATION:
2011 Habilitation (venia docendi), submitted to Department of Chemistry,
University of Konstanz
Thesis Title: Theoretical Investigations on Proteins and Determination of
Protein-Ligand Complexes
1996 - 2000: Doctorate (Dr.-Ing.), Physical Chemistry, Darmstadt University of
Technology, Germany
Thesis Title: Biomolecular Docking Using a Fuzzy Logic Based Algorithm
Thesis Advisor: Prof. Dr. Jürgen Brickmann
Summary: An algorithm was developed for the fast identification of active
sites in proteins and for placing ligands into these active sites.
1991-1996 Diploma (Master of Science) in chemistry, Darmstadt University of
Technology, Germany

Curriculum Vitae
Dr. Thomas E. Exner, Fachbereich Chemie, Universität Konstanz, 78457 Konstanz
PROFESSIONAL EMPLOYMENT:
Research:
since 10.2009 Research Associate – Department of Chemie. Universität Konstanz
10.2003-9.2009 Juniorprofessor (Assistant Professor) – Department of Chemistry,
Universität Konstanz
since 05.2006 Fellow of the Zukunftskolleg (http://www.zukunftskolleg.uni-konstanz.de/)
since 03.2005 Senior partner and Chief Technology Officer MOLCAD GmbH
(www.molcad.de)
since 08.2008 Coordination and Administration at the Universität Konstanz of the High-
Performance Computing Grid bw-GRiD of the Land Baden- Württemberg
(http://www.bw-grid.de/)
1.06.-31.09.2003 Research Associate – Department of Chemie. Universität Konstanz
2000-2003 Post-Doctoral Fellow – Department of Chemistry, University of
Saskatchewan, Saskatoon, Canada
Project Title: Quantum Chemical Investigations of Biomolecular Systems
Supervisor: Prof. Dr. P. G. Mezey
Summary: Duties include the development of a database system storing
electron density fragments and of linear scaling algorithms for the
calculation of molecular properties for biomolecular systems based on
these fragments. These properties include the total energy based on the
Hartree-Fock method, electrostatic potentials, dipole moments and partial
charges (Mulliken and Löwdin charges).
1998-2002 Research Assistant – Department of Chemistry, Darmstadt University of
Technology
Teaching:
10.2003-9.2009 Juniorprofessor (Assistant Professor) – Department of Chemistry,
Universität Konstanz
Teaching courses in theoretical and computational chemistry
1.06.-31.09.2003 Research Associate – Department of Chemie. Universität Konstanz
Teaching practical courses in physical chemistry
2000-2003 Department of Chemistry, University of Saskatchewan
Responsible for the supervision of two summer students in the field of
quantum mechanics and computational chemistry.
1998-2002 Teaching Assistant – Department of Chemistry, Darmstadt University of
Technology
Teaching practical courses in general and physical chemistry and
demonstration of second year physical chemistry laboratories. This
included the preparation and delivery of questionnaires and tutorials,
supervision of experiments, and grading exams and reports.

Curriculum Vitae
Dr. Thomas E. Exner, Fachbereich Chemie, Universität Konstanz, 78457 Konstanz
CURRENT AND FORMER WORKING GROUP:
� Dipl.-Inform. Jens Gimmler, PhD student
� Dipl.-Chem. Tim ten Brink, PhD student
� Dipl.-Chem. Andrea Frank, PhD student
� Fredrick Robin Devadoss V., PhD student
� Matthias Trautwein, Master student.
� Dr, Oliver Korb, PhD student 2004-2008 (Defense: Sep. 22, 2008, FIZ Chemie Berlin
award 2008)
� Dr. Simon Eckard, PhD student 2006-2010 (Defense: Aug. 2, 2010, summa cum laude)
HONORS AND AWARDS:
2006 Best Paper Award, ANTS 2006, 5 th International Workshop on Ant Colony
Optimization and Swarm Intelligence, September 4-7, 2006, Brussels,
Begium.
2001-2003 Feodor Lynen-Fellowship of the Alexander von Humboldt-Foundation,
post-doctoral fellowship awarded to candidates whose academic record
exceeds University standards.
2001 Kurt-Ruths-Award, awarded for excellent PhD theses in Chemistry,
Engineering and Architecture.
1997-1998 Graduate Scholarship, Land Hessen (Stipendium des Landes Hessen), PhD
scholarship awarded to graduate students whose academic record exceeds
University standards
1996 Alarich-Weiß-Award, awarded for excellent master theses in Physical
Chemistry.
1994-1996 Scholarship of the Studienstiftung des Deutschen Volkes
1994 Dr. Anton-Keller-Award, awarded for the best Vordiplom (Bachelor
Degree) in Chemistry
PROFESSIONAL MEMBERSHIPS:
� Gesellschaft Deutscher Chemiker (German Society for Chemistry)
� American Chemical Society
� Canadian Society for Chemistry
� Bunsengesellschaft für Physikalische Chemie (German Society for Physical Chemistry)
� Deutscher Hochschulverband
� Molecular Graphics and Modelling Society
� MOLCAD Network e.V. – Club for supporting junior research fellows in the fields of
molecular modeling, molecular simulations and molecular graphics
� Zukunftskolleg of the Universität Konstanz (founded in fall 2007 within the framework of
the German Excellence Initiative)

Curriculum Vitae
Dr. Thomas E. Exner, Fachbereich Chemie, Universität Konstanz, 78457 Konstanz
SCIENTIFIC COOPERATIONS:
� Tripos Inc., St. Louis, MO, USA – Development and implementation of algorithms for
the molecular modeling software SYBYL
� MOLCAD GmbH, Petersenstr. 20, 64287 Darmstadt – Main developer in the field of
molecular visualization for the software MOLCAD
� Sanofi-Aventis, Division Drug Design II, Industriepark Höchst, 65926 Frankfurt
� Prof. Christian Griesinger, Max-Planck-Institut für Biophysikalische Chemie, Göttingen
and Dr. Teresa Carlomagno, EMBL Heidelberg
� Prof. Jürgen Brickmann, MolNet Forschungsstelle, TU Darmstadt
� Prof. Paul G. Mezey, Canada Research Chair Scientific Modelling and Simulation,
Department of Chemistry and Department of Physics and Physical Oceanography,
Memorial University of Newfoundland, St. John's, NL, Canada
� Prof. Raymond A. Poirier, Department of Chemistry, Memorial University of
Newfoundland, St. John's, NL, Canada
� Prof. Thomas Stützle, IRIDIA, Université Libre de Bruxelles, Belgium
� Prof. Timothy Clark und Dr. Harald Lanig, Computer Chemie Center, Universität
Erlangen-Nürnberg
� Prof. Andreas Marx, Organische Chemie - Zelluläre Chemie, Fachbereich Chemie,
Universität Konstanz
� P.D. Katja Arndt, Instituts für Biologie III, Fakultät Biologie, Universität Freiburg
� Prof. Heiko Möller, Juniorprofessor für NMR-Spektroskopie an komplexen molekularen
Systemen, Fachbereich Chemie, Universität Konstanz, and Dr. Wolfram Gronwald,
Junior Group for Protein Structures and Interactions, Universität Regensburg.
� Prof. Michael Berthold, ALTANA Chair for Applied Computer Science, Bioinformatics
and Information Mining, and Oliver Deussen, Computergrafik und Medieninformatik,
Fachbereich Informatik und Informationswissenschaft, Universität Konstanz
OTHER PROFESSIONAL ACTIVITIES:
� Chief Technology Officer MOLCAD GmbH:
The scientific coordination of the further development of the molecular visualization
software MOLCAD was transferred into my hands in October 2005. This software is part
of the molecular modeling program package SYBYL distributed world-wide by Tripos
Inc., St. Louis, MO, USA. In this position, I am the contact person for Tripos Inc.
concerning support and requests for additional features. The implementations are
performed by employees of MOLCAD GmbH. or members of my working group.
� Member of the Zukunftkolleg:
The Zukunftskolleg offers up-and-coming scientists and scholars a creative space to
pursue outstanding research and to form their own research group. The inspiring
community of young researchers generates far-reaching ideas and research approaches:
inventive, exciting and pointing the way to the future.
� Organisation of Scientific Conference :
The Bunsenkolloquium “Chemical Bonding in Position, Momentum, and Phase Space”
took place in Konstanz on February 5-6, 2007 organized by Michael Springborg,
Universität Sarbrücken, und myself.

Curriculum Vitae
Dr. Thomas E. Exner, Fachbereich Chemie, Universität Konstanz, 78457 Konstanz
� Referee for the Swiss National Science Foundation (SNSF), German Akademic
Exchange Service (DAAD) and the German National Academic Foundation
(Studienstiftung des deutschen Volkes)
� Referee for the „Journal of Molecular Modeling“ (Springer), the „Journal of
Computational Chemistry“ (Wiley), the „Journal of Chemical Information and Modeling“
(ACS), the European Journal of Medicinal Chemisty (Elsevier), and the Journal of
Mathematical Chemistry (Springer)
� Referee for the High Performance Computing Center, University of Stuttgart
� Member of the Program Committee of the 1 st Symposium on Computational Life
Science (CompLife'05), Konstanz and the 2 nd Symposium on Computational Life Science
(CompLife'06), Cambridge, UK.
LANGUAGES
� Native language: German
� Working knowledge of English
� Basic knowledge in French
Invited Lectures since 2003:
(1) Exner, T.E. "Protein-ligand docking: Where we are and where we want to go", Physical and Chemical
Graduate School Göttingen, June 9, 2010, Göttingen, Germany
(2) Exner, T.E. "DNA Polymerase Fidelity and Human Telomeric Quadruplex Conformations", Model(l)ing
’09, September 7-11, 2009, Erlangen, Germany
(3) Exner, T.E.; Korb, O.; ten Brink, T.; and Stützle, T. "Protein-Ligand Docking Based on Ant Colony
Optimization", ACS 238 th National Meeting, August 16-20, 2009, Washington DC, USA.
(4) Exner, T.E.; Eckard, S.; and Frank, A. "Improvments of a Fragment-Based Quantum Chemical Approach:
The Border Region Problem", ACS 238 th National Meeting, August 16-20, 2009, Washington DC, USA.
(5) Exner, T.E.; "Improvments of a Fragment-Based Quantum Chemical Approach: The Border Region
Problem" Chemiedozententagung, March 8-11, 2009, Göttingen, Germany.
(6) Exner, T.E.; Korb, O.; and Stützle, T. "Protein-Ligand Docking Based on Ant Colony Optimization",
Methods of Molecular Simulations MMS08, Oktober 7-10, 2008, University of Heidelberg, Heidelberg,
Germany.
(7) Exner, T.E. "Classical/Quantum Mechanical Hybrid Methods", 5 th MATCOR Summer Shool of the
Graduate School MAINZ “Simulation of Macromolecules on Different Scales”, September 1-5, 2008, Hall
in Tirol, Austria.
(8) Exner, T.E.; Korb, O.; and Stützle, T. "Protein-Ligand Docking Based on Ant Colony Optimization", 2008
Molecular Informatics and Bioinformatics International Symposium, March 27-29, 2008, Collegium
Budapest – Institute for Advanced Study, Budapest, Hungary.
(9) Exner, T. E. "Populationsbasierte Optimierungsalgorithmen und deren Anwendung im Protein-Ligand-
Docking", Fachbereich Biowissenschaften, December 11, 2007, Universität Frankfurt, Frankfurt, Germany.
(10) Eckard, S., Mezey, P. G., and Exner, T. E. "Border Region Treatment for Fragment-Based Quantum
Chemical and Mixed Quantum Mechanical / Molecular Mechanical Approaches", 16 th Canadian
Symposium on Theoretical Chemistry, August 4-9, 2007, Memorial University of Newfoundland, St.
John's, NL, Canada.
(11) Exner, T. E. "Improvements of a Fragment-Based Quantum Chemical Approach: The Border Region
Problem", 5 th Meeting of the DFG Priority Programm 1145 Modern and Universal First-Principle Methods
for Many-Electron Systems in Chemistry and Physics, July 6, 2007, CJD, Bonn, Germany.
(12) Exner, T. E. "Theoretical Investigations on Proteins and their Interactions: Protein-Ligand and Protein-
Protein Complexes", Fachbereich Biologie, December 4, 2006, Universität Freiburg, Freiburg, Germany.
(13) Korb, O., Stützle, T., and Exner, T. E. "PLANTS: Application of Ant Colony Optimization to Structure-
Based Drug Design", ANTS 2006, 5th International Workshop on Ant Colony Optimization and Swarm
Intelligence, September 4-7, 2006, Brussels, Begium, best paper award.

Curriculum Vitae
Dr. Thomas E. Exner, Fachbereich Chemie, Universität Konstanz, 78457 Konstanz
(14) Exner, T. E. "Theoretical Investigations on Protein Interactions: Protein-Ligand, Protein-Protein, and
Protein-DNA Complexes", International Symposium on Molecular Control of Gene Expression, June 23-
24, 2006, Universität Erlangen, Erlangen, Germany.
(15) Exner, T. E. "PLANTS: Protein-Ligand ANT System", Docking and Scoring in Structure Guided Drug
Design, April 5-7, 2006, University of Southampton, Southampton, UK.
(16) Exner, T. E. "Theoretical Investigations on Proteins and their Interactions: Our State of the Art",
Fachbereich Biologie, January 19, 2006, Universität Konstanz, Konstanz, Germany.
(17) Exner, T. E. "Computational Chemistry - Scharfe Bilder und unscharfe Algorithmen", Ringvorlesung, June
13, 2005, Universität Konstanz, Konstanz, Germany.
(18) Exner, T. E. and Mezey, P. G. "Fragment-Based Approach for the Quantum Chemical Characterization of
Proteins", Bunsentagung 2005, May 5-7, 2005, Frankfurt am Main, Germany.
(19) Exner, T. E. "Identification and Characterization of Binding Sites", Computer Chemistry Center, University
of Erlangen-Nuremberg, Germany, June 14th, 2004.
(20) Exner, T. E. "New Fuzzy Logic Strategies for Bio-molecular Recognition", Computational Methods in
Toxicology and Pharmacology Integrating Internet Resources (CMTPI-2003), September 17-19, 2003,
Hotel Kinissi Palace, Thessaloniki, Greece.
Poster Presentations since 2003:
(1) Frank, A., Onila, I., and Exner, T. E. "Chemical Shift Calculations in Proteins with a Fragment-Based
Qauntum Chemical Approach", Gordon Research Conference, Computational Chemistry, August 29 -
September 3, 2010, Les Diablerets, Switzerland.
(2) Eckard, S. M. and Exner, T. E. "QM/MM Border Region Treatment: Recent Improvements", 24 rd Molecular
Modelling Workshop, March 15-16, 2010, Computer-Chemie-Centrum, Erlangen, Germany.
(3) Frank, A., Onila, I., and Exner, T. E. "Chemical Shift Calculations in Proteins with a Fragment-Based
Qauntum Chemical Approach", 24 rd Molecular Modelling Workshop, March 15-16, 2010, Computer-
Chemie-Centrum, Erlangen, Germany.
(4) ten Brink, T. and Exner, T. E. "A Combined Combinatorial and pKA-based Approach for Ligand
Protonation States", 5 th German Conference on Chemoinformatics, November 8-10, 2009, Goslar,
Germany
(5) Hesser, G., Korb, O., Monecke, P., Stützle, T., and Exner, T. E. "pharmacophore: Multiple Flexible Ligand
Alignment Based on Ant Colony Optimization", 5 th German Conference on Chemoinformatics, November
8-10, 2009, Goslar, Germany
(6) Eckard, S. M. and Exner, T. E. "Saturating Dangling Bonds with GHO – Recent Developments",
Model(l)ing ’09, September 7-9, 2009, Erlangen, Germany.
(7) ten Brink, T. and Exner, T. E. "Systematic Studies on the Influence of Ligand Protonation in Protein-
Ligand Docking", Model(l)ing ’09, September 7-9, 2009, Erlangen, Germany.
(8) Eckard, S. M. and Exner, T. E. "Saturating Dangling Bonds with GHO – Recent Developments", 23 rd
Molecular Modelling Workshop, September 6-7, 2009, Computer-Chemie-Centrum, Erlangen, Germany.
(9) Gimmler, J., Gronwald, W., Möller, H., and Exner, T. E "Protein structure calculation with a Max-Min Ant
System", 4 th German Conference on Chemoinformatics, November 9-11, 2008, Goslar, Germany, best
poster award.
(10) ten Brink, T. and Exner, T. E. "Ligand protonation states and stereoisomers in virtual screening", 4 th
German Conference on Chemoinformatics, November 9-11, 2008, Goslar, Germany.
(11) Korb, O., ten Brink, T., and Exner, T.E. "New and Improved Features of the Docking Software PLANTS",
4 th German Conference on Chemoinformatics, November 9-11, 2008, Goslar, Germany.
(12) Gimmler, J., Gronwald, W., Möller, H., and Exner, T. E. "Protein structure calculation with a Max-Min Ant
System", 30. GDCh Fachgruppentagung Magnetische Resonanzspektroskopie, September 22-25, 2008,
Regensburg, Germany.
(13) Brickmann, J., Zerara, M., Kretschmer, R., and Exner, T. E. "Parametrization of the molecular free energy
surface density (MolFESD) for different solvents and brain-blood barrier partitioning ", 3 nd German
Conference on Chemoinformatics, November 11-13, 2007, Goslar, Germany.
(14) ten Brink, T. and Exner, T. E. "The Influence of Protonation in Protein-Ligand Docking", 3 nd German
Conference on Chemoinformatics, November 11-13, 2007, Goslar, Germany.
(15) Exner, T. E. "Comparison of the Incorporation of Watson-Crick Complementary and Mismatched
Nucleotides Catalyzed by DNA Polymerase I", High Performance Computing in Science and Engineering,

Curriculum Vitae
Dr. Thomas E. Exner, Fachbereich Chemie, Universität Konstanz, 78457 Konstanz
10th Results and Review Workshop of the HLRS, October 4 - 5, 2007 at the High Performance Computing
Center Stuttgart, Allmandring 30, 70569 Stuttgart.
(16) Gimmler, J., Möller, H., and Exner, T. E. "Protein structure calculation with a Max-Min Ant System", 29.
GDCh Fachgruppentagung Magnetische Resonanzspektroskopie, September 26-29, 2007, Göttingen,
Germany.
(17) Riemann, R. N., Exner, T. E., and Brickmann, J. "Fast calculation of partial charges based on
electronegativity equalization and polarization effects", Wissenschaftsforum Chemie 2007, September 16-
19, 2007, Universität Ulm, Ulm, Germany.
(18) Exner, T. E., Zerara, M., Kretschmer, R., Exner, T. E., Jäger, R., and Brickmann, J. "Parametrization of the
Molecular Free Energy Surface Density (MolFESD) for Various Systems", 21 st Darmstädter Molecular
Modelling Workshop, May 15-16, 2007, Computer-Chemie-Centrum, Erlangen, Germany.
(19) Korb, O., Stützle, T., and Exner, T. E. "When Ants Design Scoring Functions", 21 st Darmstädter Molecular
Modelling Workshop, May 15-16, 2007, Computer-Chemie-Centrum, Erlangen, Germany.
(20) Gimmler, J., Möller, H., and Exner, T. E. "Protein Structure Calculation with a Max-Min Ant System", 21 st
Darmstädter Molecular Modelling Workshop, May 15-16, 2007, Computer-Chemie-Centrum, Erlangen,
Germany, best poster award.
(21) ten Brink, T. and Exner, T. E. "The Influence of Ligand Protonation in Protein-Ligand Docking", 21 st
Darmstädter Molecular Modelling Workshop, May 15-16, 2007, Computer-Chemie-Centrum, Erlangen,
Germany.
(22) Korb, O., Stützle, T., and Exner, T. E. "PLANTS: Protein-Ligand ANT System", 2 nd German Conference
on Chemoinformatics, November 12-14, 2006, Goslar, Germany.
(23) Eckard, S. and Exner, T. E. " Quantum Chemical Calculations for Proteins: The Adjustable Density Matrix
Assembler", 2 nd German Conference on Chemoinformatics, November 12-14, 2006, Goslar, Germany, best
poster award.
(24) Eckard, S. and Exner, T. E. "Quantum Chemical Calculations for Proteins: The Adjustable Density Matrix
Assembler", Symposium 2006 of the DFG Priority Program 1145, June 26-28, 2006, Bad Herrenalb,
Germany.
(25) Korb, O., Stützle, T., and Exner, T. E. "Consumer Graphics Hardware: A Powerful Resource for
Computational Chemistry", Bunsentagung 2006, May 25-27, 2006, Erlangen, Germany.
(26) Eckard, S. and Exner, T. E. "Border-Region Treatment in the Field-Adapted Adjustable Density Matrix
Assembler", Bunsentagung 2006, May 25-27, 2006, Erlangen, Germany.
(27) ten Brink, T., Korb, O., and Exner, T. E. "Parameterization of a simple and effective scoring function for
protein-protein docking", 20. Darmstädter Molecular Modelling Workshop, May 23-24, 2006, Computer-
Chemie-Centrum, Erlangen, Germany.
(28) Korb, O., Stützle, T., and Exner, T. E. " PLANTS: Protein-Ligand ANT System – Results and
Comparison", 20. Darmstädter Molecular Modelling Workshop, May 23-24, 2006, Computer-Chemie-
Centrum, Erlangen, Germany.
(29) Gimmler, J. and Exner, T. E. "A heuristic 3D-structure-based protein alignment algorithm", 20.
Darmstädter Molecular Modelling Workshop, May 23-24, 2006, Computer-Chemie-Centrum, Erlangen,
Germany.
(30) Eckard, S. and Exner, T. E. "Border-Region Treatment in the Field-Adapted Adjustable Density Matrix
Assembler", 20. Darmstädter Molecular Modelling Workshop, May 23-24, 2006, Computer-Chemie-
Centrum, Erlangen, Germany.
(31) Gimmler, J., Stützle, T., and Exner, T. E. "Continuous global optimization: Finding the right algorithm for a
problem", 19. Darmstädter Molecular Modelling Workshop, May 3-4,2005, Computer-Chemie-Centrum,
Erlangen, Germany.
(32) Korb, O., Stützle, T., Kast, S. M., and Exner, T. E. "When Ants Dock Molecules", 19. Darmstädter
Molecular Modelling Workshop, May 3-4,2005, Computer-Chemie-Centrum, Erlangen, Germany, best
poster award.
(33) Korb, O., Stützle, T., Kast, S. M., and Exner, T. E. "Protein-ligand Docking: The Energy Landscape View",
Bunsentagung 2005, May 5-7, 2005, Frankfurt am Main, Germany.
(34) Jouaux, E. M., Exner, T. E., and Arndt, K. M. "Targeting against Myc:Max coiled coil domain for specific
inhibition", Katzir Conference on Molecular Perspectives on Protein-Protein-Interactions, November 6-10,
2005, Eilat, Israel.

Curriculum Vitae
Dr. Thomas E. Exner, Fachbereich Chemie, Universität Konstanz, 78457 Konstanz
(35) Korb, O., Stützle, T., Kast, S. M., and Exner, T. E. "On the Occurence of Docking Funnels: Identification
and Characterization", 18th Molecular Modelling Workshop, May 18-19, 2004, Computer-Chemie-
Centrum, Erlangen, Germany.

Curriculum Vitae
Dr. Thomas E. Exner, Fachbereich Chemie, Universität Konstanz, 78457 Konstanz
PUBLICATIONS:
(1) 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).
(2) 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.Mag.Res. 208, 167-170 (2010).
(3) 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).
(4) 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. 50,
1669-1681 (2010).
(5) 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).
(6) Korb, O.; Möller, H. M.; Exner, T. E. "NMR-guided Molecular Docking of a Protein-
Peptide Complex Based on Ant Colony Optimization", ChemMedChem 5, 1001-1006
(2010).
(7) 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).
(8) ten Brink, T.; Exner, T. E. "The Influence of Protonation States on Protein-Ligand
Docking Results", J.Chem.Inf.Model. 49, 1525-1546 (2009).
(9) 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).
(10) Exner, T. E. "Insights into the High Fidelity of a DNA Polymerase I Mutant",
J.Mol.Model. 15, 1271-1280 (2009).
(11) Eckard, S.; Exner, T. E. "Improvements for the Generalized Hybrid Orbital Method for
Fragment-Based Quantum Chemical Approaches", Int.J.Quatum.Chem. 109, 1451–1463
(2009).
(12) 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).
(13) Jouaux, E. M.; Timm, B.; Arndt, K. M.; Exner, T. E. "Optimization of a Myc-Interfering
Peptide Based on Molecular Dynamics Simulations", J.Peptid.Sci. 15, 5-15 (2009).
(14) Zerara, M.; Brickmann, J.; Kretschmer, R.; Exner, T. E. "Parametrization of the molecular
free energy surface density (MolFESD) for the prediction of n-octanol, alkane and
cyclohexane / water as well as brain-blood partition coefficients", J.Comp.-Aided Mol.
Design 23, 105-111 (2009).
(15) 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).
(16) Korb, O.; Stützle, T.; Exner, T. E. "An ant colony optimization approach to flexible
protein-ligand docking", Swarm Intell. 1, 115-134 (2007).
(17) 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).

Curriculum Vitae
Dr. Thomas E. Exner, Fachbereich Chemie, Universität Konstanz, 78457 Konstanz
(18) 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).
(19) Eckard, S.; Exner, T. E. "Generalized Hybrid Orbitals in the FA-ADMA Method",
Z.Phys.Chem. 220, 927-944 (2006).
(20) 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).
(21) 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).
(22) 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).
(23) Exner, T. E.; Mezey, P. G. "The Field-Adapted ADMA Approach: Introducing Point
Charges", J.Phys.Chem.A 108, 4301-4309 (2004).
(24) 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).
(25) Exner, T. E.; Keil, M.; Brickmann, J. "New Fuzzy Logic Strategies for Bio-molecular
Recognition", SAR QSAR Environ.Res. 14, 421-431 (2003).
(26) Exner, T. E.; Mezey, P. G. "Ab Initio Quality Properties for Macromolecules Using the
ADMA Approach", J.Comp.Chem. 24, 1980-1986 (2003).
(27) 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).
(28) Exner, T. E.; Keil, M.; Brickmann, J. "Pattern Recognition Strategies for Molecular
Surfaces II. Surface Complementarity", J.Comp.Chem. 23, 1188-1197 (2002).
(29) 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).
(30) Exner, T. E.; Mezey, P. G. "Comparison of Nonlinear Transformation Methods for
Electron Density Approximation", J.Phys.Chem.A 106, 5504-5509 (2002).
(31) Exner, T. E.; Brickmann, J. "The Identification of Complementarity of Molecular
Surfaces Using Fuzzy Set Theory", J.Mol.Model. 7, 370-373 (2001).
(32) Brickmann, J.; Keil, M.; Exner, T. E.; Marhöfer, R. "Molecular Graphics: Trends and
Perspectives", J.Mol.Model. 6, 328-340 (2000).
(33) Exner, T. E.; Brickmann, J. "Molecular Shape Recognition Using Fuzzy Logic
Strategies", Match - Communications in Mathematical and in Computer Chemistry 38,
53-80 (1998).
(34) Exner, T. E.; Keil, M.; Moeckel, G.; Brickmann, J. "Identification of Substrate Channels
and Protein Cavities", J.Mol.Model. 4, 340-343 (1998).
(35) Keil, M.; Exner, T. E.; Brickmann, J. "Characterisation of Protein-Ligand Interfaces:
Separating Surface", J.Mol.Model. 4, 335-339 (1998) .
(36) Exner, T. E.; Brickmann, J. "Fuzzy Logic Strategien zur Behandlung der Molekularen
Erkennung", GIT Labor-Fachzeitschrift 11, 1144-1146 (1998).
(37) Exner, T. E.; Brickmann, J. "New docking algorithm based on fuzzy set theory",
J.Mol.Model. 3, 321-324 (1997).

Curriculum Vitae
Dr. Thomas E. Exner, Fachbereich Chemie, Universität Konstanz, 78457 Konstanz
Book Chapters:
(1) 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.
(2) 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.
(3) 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.
(4) 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.
(5) 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.
Proceedings (peer reviewed):
(1) ten Brink, T. and Exner, T. E. "Ligand protonation states and stereoisomers in virtual
screening" Chem.Central J. 3 (Suppl I), P14 (2009).
(2) 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).
(3) Gimmler, J., Gronwald, W., Möller, H., and Exner, T. E. " Protein structure calculation
with a max-min ant system" Chem.Central J. 3 (Suppl I), P52 (2009).
(4) Exner, T. E., Korb, O., ten Brink, T., and Stützle, T. "Protein-ligand docking based on ant
colony optimization" in Abstracts of Papers; 238th ACS National Meeting, Washington,
DC, United States, August 16-20, 2009, (2009).
(5) Exner, T. E., Eckard, S.; and Frank, A. "Improvements of a fragment-based quantum
chemical approach: The border region problem" in Abstracts of Papers; 238th ACS
National Meeting, Washington, DC, United States, August 16-20, 2009, (2009).
(6) 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).
(7) ten Brink, T. and Exner, T. E. "The influence of protonation in protein-ligand docking"
Chem.Central J. 2 (Suppl I), P12 (2008).
(8) 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).

Curriculum Vitae
Dr. Thomas E. Exner, Fachbereich Chemie, Universität Konstanz, 78457 Konstanz
(9) 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).
(10) 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).
(11) 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).
(12) 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).