Gerhard Klebe

Publication Activity (10 Years)

Years Active: 1989-2020
Publications (10 Years): 7

Top Topics

Similarity Retrieval

Protein Structure

Top Venues

J. Chem. Inf. Model.

IEEE ACM Trans. Comput. Biol. Bioinform.

J. Cheminformatics

WIREs Data Mining Knowl. Discov.

Publications

Tobias Hüfner-Wulsdorf, Gerhard Klebe
Protein-Ligand Complex Solvation Thermodynamics: Development, Parameterization, and Testing of GIST-Based Solvent Functionals. J. Chem. Inf. Model. 60 (3) (2020)
Tobias Hüfner-Wulsdorf, Gerhard Klebe
Advancing GIST-Based Solvent Functionals through Multiobjective Optimization of Solvent Enthalpy and Entropy Scoring Terms. J. Chem. Inf. Model. 60 (12) (2020)
Tobias Hüfner-Wulsdorf, Gerhard Klebe
Role of Water Molecules in Protein-Ligand Dissociation and Selectivity Discrimination: Analysis of the Mechanisms and Kinetics of Biomolecular Solvation Using Molecular Dynamics. J. Chem. Inf. Model. 60 (3) (2020)
Michael Betz, Tobias Wulsdorf, Stefan G. Krimmer, Gerhard Klebe
Impact of Surface Water Layers on Protein-Ligand Binding: How Well Are Experimental Data Reproduced by Molecular Dynamics Simulations in a Thermolysin Test Case? J. Chem. Inf. Model. 56 (1) (2016)
Matthias Leinweber, Thomas Fober, Marc Strickert, Lars Baumgärtner, Gerhard Klebe, Bernd Freisleben, Eyke Hüllermeier
CavSimBase: A Database for Large Scale Comparison of Protein Binding Sites. IEEE Trans. Knowl. Data Eng. 28 (6) (2016)
Timo Krotzky, Christian Grunwald, Ute Egerland, Gerhard Klebe
Large-Scale Mining for Similar Protein Binding Pockets: With RAPMAD Retrieval on the Fly Becomes Real. J. Chem. Inf. Model. 55 (1) (2015)
Stefan G. Krimmer, Gerhard Klebe
Thermodynamics of protein-ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data. J. Comput. Aided Mol. Des. 29 (9) (2015)
Timo Krotzky, Gerhard Klebe
A new method for rapid comparison of protein binding pockets by capturing spatial distributions. J. Cheminformatics 6 (S-1) (2014)
Michiel Stock, Thomas Fober, Eyke Hüllermeier, Serghei Glinca, Gerhard Klebe, Tapio Pahikkala, Antti Airola, Bernard De Baets, Willem Waegeman
Identification of Functionally Related Enzymes by Learning-to-Rank Methods. IEEE ACM Trans. Comput. Biol. Bioinform. 11 (6) (2014)
Timo Krotzky, Thomas Rickmeyer, Thomas Fober, Gerhard Klebe
Extraction of Protein Binding Pockets in Close Neighborhood of Bound Ligands Makes Comparisons Simple Due to Inherent Shape Similarity. J. Chem. Inf. Model. 54 (11) (2014)
Timo Krotzky, Thomas Fober, Eyke Hüllermeier, Gerhard Klebe
Extended Graph-Based Models for Enhanced Similarity Search in Cavbase. IEEE ACM Trans. Comput. Biol. Bioinform. 11 (5) (2014)
Michiel Stock, Thomas Fober, Eyke Hüllermeier, Serghei Glinca, Gerhard Klebe, Tapio Pahikkala, Antti Airola, Bernard De Baets, Willem Waegeman
Identification of functionally related enzymes by learning-to-rank methods. CoRR (2014)
Thomas Fober, Marco Mernberger, Gerhard Klebe, Eyke Hüllermeier
Graph-based methods for protein structure comparison. WIREs Data Mining Knowl. Discov. 3 (5) (2013)
Timo Krotzky, Thomas Fober, Marco Mernberger, Gerhard Klebe, Eyke Hüllermeier
Extended graph-based models for enhanced similarity retrieval in Cavbase. J. Cheminformatics 5 (S-1) (2013)
Serghei Glinca, Gerhard Klebe
Cavities Tell More than Sequences: Exploring Functional Relationships of Proteases via Binding Pockets. J. Chem. Inf. Model. 53 (8) (2013)
Matthias Leinweber, Lars Baumgärtner, Marco Mernberger, Thomas Fober, Eyke Hüllermeier, Gerhard Klebe, Bernd Freisleben
GPU-based Cloud computing for comparing the structure of protein binding sites. DEST (2012)
Gerhard Klebe
On the validity of popular assumptions in computational drug design. J. Cheminformatics 3 (S-1) (2011)
Gerd Neudert, Gerhard Klebe
: A Knowledge-Based Scoring Function for the Assessment of Protein-Ligand Complexes. J. Chem. Inf. Model. 51 (10) (2011)
Gerd Neudert, Gerhard Klebe
fconv: format conversion, manipulation and feature computation of molecular data. Bioinform. 27 (7) (2011)
Marco Mernberger, Gerhard Klebe, Eyke Hüllermeier
SEGA: Semiglobal Graph Alignment for Structure-Based Protein Comparison. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (5) (2011)
Andreas Spitzmüller, Hans F. G. Velec, Gerhard Klebe
MiniMuDS: A New Optimizer using Knowledge-Based Potentials Improves Scoring of Docking Solutions. J. Chem. Inf. Model. 51 (6) (2011)
Thomas Fober, Serghei Glinca, Gerhard Klebe, Eyke Hüllermeier
Superposition and Alignment of Labeled Point Clouds. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (6) (2011)
Paul Czodrowski, Chresten R. Søndergaard, Sebastian Dohm, Gerhard Klebe, Jens E. Nielsen
LigpKa - a database of pKa values for small molecule ligands designed for the use in structure-based pKa calculations. J. Cheminformatics 3 (S-1) (2011)
Thomas Fober, Marco Mernberger, Gerhard Klebe, Eyke Hüllermeier
Efficient Similarity Retrieval of Protein Binding Sites based on Histogram Comparison. GCB (2010)
Patrick Pfeffer, Thomas Fober, Eyke Hüllermeier, Gerhard Klebe
GARLig: A Fully Automated Tool for Subset Selection of Large Fragment Spaces via a Self-Adaptive Genetic Algorithm. J. Chem. Inf. Model. 50 (9) (2010)
Thomas Fober, Gerhard Klebe, Eyke Hüllermeier
Efficient Construction of Multiple Geometrical Alignments for the Comparison of Protein Binding Sites. ISDA (2009)
Oliver Koch, Jason C. Cole, Peter Block, Gerhard Klebe
Secbase: Database Module To Retrieve Secondary Structure Elements with Ligand Binding Motifs. J. Chem. Inf. Model. 49 (10) (2009)
Thomas Fober, Marco Mernberger, Gerhard Klebe, Eyke Hüllermeier
Evolutionary construction of multiple graph alignments for the structural analysis of biomolecules. Bioinform. 25 (16) (2009)
Hao Fan, John J. Irwin, Benjamin M. Webb, Gerhard Klebe, Brian K. Shoichet, Andrej Sali
Molecular Docking Screens Using Comparative Models of Proteins. J. Chem. Inf. Model. 49 (11) (2009)
Alexander Hillebrecht, Gerhard Klebe
Use of 3D QSAR Models for Database Screening: A Feasibility Study. J. Chem. Inf. Model. 48 (2) (2008)
Paul Czodrowski, Christoph A. Sotriffer, Gerhard Klebe
Atypical Protonation States in the Active Site of HIV-1 Protease: A Computational Study. J. Chem. Inf. Model. 47 (4) (2007)
Todd J. Dolinsky, Paul Czodrowski, Hui Li, Jens E. Nielsen, Jan H. Jensen, Gerhard Klebe, Nathan A. Baker
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Nils Weskamp, Eyke Hüllermeier, Daniel Kuhn, Gerhard Klebe
Multiple Graph Alignment for the Structural Analysis of Protein Active Sites. IEEE ACM Trans. Comput. Biol. Bioinform. 4 (2) (2007)
Eyke Hüllermeier, Nils Weskamp, Gerhard Klebe, Daniel Kuhn
Graph Alignment: Fuzzy Pattern Mining for the Structural Analysis of Protein Active Sites. FUZZ-IEEE (2007)
Peter Block, Christoph A. Sotriffer, Ingo Dramburg, Gerhard Klebe
AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB. Nucleic Acids Res. 34 (Database-Issue) (2006)
Alexander Weber, Markus Böhm, Claudiu T. Supuran, Andrea Scozzafava, Christoph A. Sotriffer, Gerhard Klebe
3D QSAR Selectivity Analyses of Carbonic Anhydrase Inhibitors: Insights for the Design of Isozyme Selective Inhibitors. J. Chem. Inf. Model. 46 (6) (2006)
Nils Weskamp, Daniel Kuhn, Eyke Hüllermeier, Gerhard Klebe
Efficient similarity search in protein structure databases by k-clique hashing. Bioinform. 20 (10) (2004)
Nils Weskamp, Eyke Hüllermeier, Daniel Kuhn, Gerhard Klebe
Graph Alignments: A New Concept to Detect Conserved Regions in Protein Active Sites. German Conference on Bioinformatics (2004)
Katrin Kupas, Alfred Ultsch, Gerhard Klebe
Comparison of substructural epitopes in enzyme active sites using self-organizing maps. J. Comput. Aided Mol. Des. 18 (11) (2004)
Jonas Boström, Markus Böhm, Klaus Gundertofte, Gerhard Klebe
Receptor Antagonists. J. Chem. Inf. Comput. Sci. 43 (3) (2003)
Nils Weskamp, Daniel Kuhn, Eyke Hüllermeier, Gerhard Klebe
Efficient Similarity Search in Protein Structure Databases: Improving Cliqae-Detection through Clique Hashing. German Conference on Bioinformatics (2003)
J. Willem M. Nissink, Marcel L. Verdonk, Gerhard Klebe
Simple knowledge-based descriptors to predict protein-ligand interactions. Methodology and validation. J. Comput. Aided Mol. Des. 14 (8) (2000)
Gerhard Klebe, Thomas Mietzner, Frank Weber
Methodological developments and strategies for a fast flexible superposition of drug-size molecules. J. Comput. Aided Mol. Des. 13 (1) (1999)
Gerhard Klebe, Ute Abraham
Comparative Molecular Similarity Index Analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries. J. Comput. Aided Mol. Des. 13 (1) (1999)
J. Willem M. Nissink, Marcel L. Verdonk, Jan Kroon, Thomas Mietzner, Gerhard Klebe
Superposition of molecules: Electron density fitting by application of fourier transforms. J. Comput. Chem. 18 (5) (1997)
Christof H. Schwab, Sandra Handschuh, Andreas Teckentrup, Markus Wagener, Jens Sadowski, Johann Gasteiger, Paul Levi, T. Will, Andreas Zell, H. Siemens, Gerhard Klebe, Thomas Mietzner, Frank Weber, Gerhard Barnickel, Soheila Anzali, Michael Krug
A Systemsatic Approach to Finding New Lead Structures Having Biological Activity. German Conference on Bioinformatics - Selected Papers (1996)
Gerhard Klebe, Thomas Mietzner, Frank Weber
Different approaches toward an automatic structural alignment of drug moleculars: Applications to sterol mimics, thrombin and thermolysin inhibitors. J. Comput. Aided Mol. Des. 8 (6) (1994)
Gerhard Klebe, Thomas Mietzner
A fast and efficient method to generate biologically relevant conformations. J. Comput. Aided Mol. Des. 8 (5) (1994)
Jens Sadowski, Johann Gasteiger, Gerhard Klebe
Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures. J. Chem. Inf. Comput. Sci. 34 (4) (1994)
Gerhard Klebe
Durch die Berechnung von Moleküleigenschaften zum gezielten Entwurf von neuen Wirkstoffen. Supercomputer (1989)