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Fachbereich Chemie
     
DR. OLIVER KORB 


Postal:
   Cambridge Crystallographic Data Centre
   12 Union Road
   Cambridge, UK
   CB2 1EZ
   Email: korb AT ccdc.cam.ac.uk
PhD Thesis: Efficient Ant Colony Optimization Algorithms for Structure- and Ligand-Based Drug Design
Diploma Thesis: Heuristiken zur approximativen Lösung
des globalen rigiden
Protein-Ligand-Docking-Problems
Student Research Project: Das Traveling Salesman Problem im GAILS-Framework:
Integration und Analyse
Personal
10/1999 − 10/2004 Student in Computer Science, Darmstadt University of Technology
01/2005 − 09/2008 Research Assistant at TCD
10/2008 − 12/2010 Postdoc at the Cambridge Crystallographic Data Centre
since 10/2009 Research Associate at Clare College, University of Cambridge
since 2011 Scientific Software Engineer at the Cambridge Crystallographic Data Centre
Research Interests
− GOLD (Genetic Optimisation for Ligand Docking)
− Docking to crystal structures of small molecules
− PLANTS: Protein-Ligand ANT System (protein-ligand docking considering ligand and protein flexibility)
− Protein-Ligand Docking (new methods based on SLS)
− Stochastic Local Search ( Ant Colony Optimization (ACO), Iterated Local Search (ILS) etc.)
− GPGPU: General-Purpose computation on GPUs (PLANTSGPU, GPU-accelerated protein-ligand docking)
− Computer Graphics and OpenGL
Oral Presentations
1) Korb, O., Stützle, T., Exner, T. E. "PLANTS: Protein-Ligand ANT System", 20th Molecular Modelling Workshop, May 23-24, 2006, Computer-Chemie-Centrum, Erlangen, Germany. (abstract)
2) Korb, O., Stützle, T., Exner, T. E. "PLANTS: Application of Ant Colony Optimization to Structure-Based Drug Design", Ant Colony Optimization and Swarm Intelligence, 5th International Workshop, ANTS 2006, September 4-7, 2006, Universite Libre de Bruxelles, Brussels, Belgium.
3) Korb, O., Stützle, T., Exner, T. E. "Speeding Up Molecular Docking Calculations Using Consumer Graphics Hardware", 2nd German Conference on Chemoinformatics, November 12-14, 2006, Goslar, Germany. (abstract)
4) Korb, O., Stützle, T., Exner, T. E. "Application of Ant Colony Optimization to Structure-Based Drug Design", Molecular Docking, Complexity and Optimization (MDCO 2007) - Satellite Conference of the European Conference on Complex System (ECCS 2007), October 4, 2007, Dresden, Germany.
5) Korb, O. "Efficient Ant Colony Optimization Algorithms for Structure- and Ligand-Based Drug Design", 4th German Conference on Chemoinformatics, November 9-11, 2008, Goslar, Germany.
6) Korb, O. "Ensemble Docking Revisited", UK-QSAR meeting, October 22, 2009, Syngenta, Bracknell, UK.
7) Korb, O. "Ensemble Docking Revisited", OpenEye EuroCUP IV, April 28-30, 2010, Bergisch-Gladbach, Germany.
8) Korb, O. "Broadening the Horizon of Molecular Docking", 5th Sheffield Conference on Chemoinformatics, July 13-15, 2010, Sheffield, UK.
9) Korb, O., Cole, J. "Ant Colony Optimisation for Ligand Docking", ANTS 2010, September 8-10, 2010, Brussels, Belgium.
Poster Presentations
1) Korb, O., Duchstein, P., Borosch, T., Kast, S. M., Brickmann, J. "Analysing protein channels: From automatic detection to path exploration", 17th Molecular Modelling Workshop, May 27-28, 2003, Computer-Chemie-Centrum, Erlangen, Germany. (abstract)
2) Korb, O., Stützle, T., Kast, S. M., 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. (abstract)
3) Korb, O., Stützle, T., Kast, S. M., Exner, T. E. "When Ants Dock Molecules", 19th Molecular Modelling Workshop, May 3-4, 2005, Computer-Chemie-Centrum, Erlangen, Germany.
(poster award) (abstract)
4) Korb, O., Stützle, T., Kast, S. M., Exner, T. E. "Protein-Ligand Docking: The Energy Landscape View", Bunsentagung, May 5-7, 2005, Frankfurt, Germany. (abstract)
5) Korb, O., Stützle, T., Exner, T. E. "PLANTS: Protein-Ligand ANT System. Results and Comparison", Docking and Scoring in Structure Guided Drug Design, April 5-7, 2006, Southampton, UK. (abstract)
6) ten Brink, T., Korb, O., Exner, T. E. "Parameterization of a simple and efficient scoring function for protein-protein docking", 20th Molecular Modelling Workshop, May 23-24, 2006, Computer-Chemie-Centrum, Erlangen, Germany. (abstract)
7) Korb, O., Stützle, T., Exner, T. E. "PLANTS: Protein-Ligand ANT System. Results and Comparison", 20th Molecular Modelling Workshop, May 23-24, 2006, Computer-Chemie-Centrum, Erlangen, Germany. (abstract)
8) Korb, O., Stützle, T., Exner, T. E. "Consumer Graphics Hardware: A Powerful Resource for Computational Chemistry", Bunsentagung, May 25-27, 2006, Erlangen, Germany. (abstract)
9) Korb, O., Stützle, T., Exner, T. E. "PLANTS: Application of Ant Colony Optimization to Structure-Based Drug Design", Ant Colony Optimization and Swarm Intelligence, 5th International Workshop, ANTS 2006, September 4-7, 2006, Universite Libre de Bruxelles, Brussels, Belgium.
10) Korb, O., Stützle, T., Exner, T. E. "PLANTS: Protein-Ligand ANT System", 2nd German Conference on Chemoinformatics, November 12-14, 2006, Goslar, Germany. (abstract)
11) Korb, O., Stützle, T., Exner, T. E. "When Ants Design Scoring Functions", 21st Molecular Modelling Workshop, May 15-16, 2007, Computer-Chemie-Centrum, Erlangen, Germany.
12) Korb, O., Stützle, T., Exner, T. E. "Multi-Body Interactions in Molecular Docking: Treatment of Water Molecules and Multiple Ligands", 3rd German Conference on Chemoinformatics, November 11-13, 2007, Goslar, Germany. (abstract)
Refereed Conference Articles
1) Korb, O., Stützle, T., Exner, T. E. (2006)   PLANTS: Application of Ant Colony Optimization to Structure-Based Drug Design.   In M. Dorigo, L. M. Gambardella, M. Birattari, A. Martinoli, R. Poli, T. Stützle (Eds.) Ant Colony Optimization and Swarm Intelligence, 5th International Workshop, ANTS 2006, LNCS 4150, pp. 247-258.
(best paper award) http://dx.doi.org/10.1007/11839088_22
2) Korb, O., Cole, J. (2010)   Ant Colony Optimisation for Ligand Docking.   In M. Dorigo et al. (Eds.) Swarm Intelligence, LNCS 6234, pp. 72-83. http://dx.doi.org/10.1007/978-3-642-15461-4_7
Communications
1) Korb, O., Wood, P. (2010)   Prediction of framework-guest systems using molecular docking.   Chemical Communications, 46(19), pp. 3318-3320. http://dx.doi.org/10.1039/C003080E
Book Chapters
1) Cole, J. C., Korb, O., Olsson, T. S. G., Liebeschuetz, J. W. (2011)   The basis for target-based virtual screening: Protein structures.   Virtual Screening. Principles, Challenges and Practical Guidelines, Eds. Christoph Sotriffer, Pubs. Wiley, pp. 87-114. http://dx.doi.org/10.1002/9783527633326
Journal Articles
1) Korb, O., Stützle, T., Exner, T. E. (2007)   An Ant Colony Optimization Approach to Flexible Protein-Ligand Docking.   Swarm Intelligence,1(2), pp. 115-134. http://dx.doi.org/10.1007/s11721-007-0006-9
2) Keil, M., Marhöfer, R. J., Rohwer, A., Selzer, P. M., Brickmann, J., Korb, O., Exner, T. E. (2009)   Molecular visualization in the rational drug design process.   Frontiers in Bioscience, 14, pp. 2559-2583. abstract
3) Korb, O., Stützle, T., Exner, T. E. (2009)   Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS.   Journal of Chemical Information and Modeling, 49(1), pp. 84-96. http://dx.doi.org/10.1021/ci800298z
4) Zonta, N., Cozza, G., Gianoncelli, A., Korb, O., Exner, T.E., Meggio, F., Zagotto, G., Moro, S. (2009)   Scouting Novel Protein Kinase A (PKA) Inhibitors by Using a Consensus Docking-Based Virtual Screening Approach.   Letters in Drug Design and Discovery, 6(5), pp. 327-336.
5) Korb, O., Möller, H., Exner, T.E. (2010)   NMR-Guided Molecular Docking of a Protein-Peptide Complex Based on Ant Colony Optimization   ChemMedChem, 6(7), pp. 1001-1006. http://dx.doi.org/10.1002/cmdc.201000090
6) Korb, O., Monecke, P., Hessler, G., Stützle, T., Exner, T.E. (2010)   pharmACOphore: Multiple Flexible Ligand Alignment Based on Ant Colony Optimization   Journal of Chemical Information and Modeling, 50(9), pp. 1669-1681. http://dx.doi.org/10.1021/ci1000218
7) Korb, O., Stützle, T., Exner, T.E. (2011)   Accelerating Molecular Docking Calculations Using Graphics Processing Units   Journal of Chemical Information and Modeling, 51(4), pp. 865-876. http://dx.doi.org/10.1021/ci100459b
8) Verdonk, M. L., Giangreco, I., Hall, R. J., Korb, O., Mortenson, P. N., and Murray, C. W. (2011)   Docking performance of fragments and drug-like compounds   Journal of Medicinal Chemistry, 54 (15), pp. 5422-5431.. http://dx.doi.org/10.1021/jm200558u
9) Korb, O., McCabe, P., and Cole, J. (2011)   The Ensemble Performance Index: An Improved Measure for Assessing Ensemble Pose Prediction Performance   Journal of Chemical Information and Modeling, 51 (11), pp 2915-2919.. http://dx.doi.org/10.1021/ci2002796
10) Korb, O., ten Brink, T., Devadoss, F.R., Keil, M., Exner, T.E. (2012)   Are Predefined Decoy Sets of Ligand Poses Able to Quantify Scoring Function Accuracy?   Journal of Computer-Aided Molecular Design, 26 (2), pp 185-197. .http://dx.doi.org/10.1007/s10822-011-9539-5
11) Liebeschuetz, J., Cole, J.C., Korb, O. (2012)   Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test   Journal of Computer-Aided Molecular Design, Accepted..
12) Korb, O., Olsson, T.S.G., Bowden, S.J., Hall, R.J., Verdonk, M.L., Liebeschuetz, J., Cole, J.C. (2012)   Potential and Limitations of Ensemble Docking   Journal of Chemical Information and Modeling, Accepted..
13) Taylor, R., Cole, J.C., Cosgrove, D.A., Gardiner, E.J., Gillet, V.J., Korb, O. (2012)   Development and validation of an improved algorithm for overlaying flexible molecules   Journal of Computer-Aided Molecular Design, Accepted. .http://dx.doi.org/10.1007/s10822-012-9573-y
thomas.exner@uni-konstanz.de last update: May 08, 2012