Gerhard Klebe

According to our database1, Gerhard Klebe
  • authored at least 47 papers between 1989 and 2016.
  • has a "Dijkstra number"2 of four.

Timeline

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Bibliography

2016
CavSimBase: A Database for Large Scale Comparison of Protein Binding Sites.
IEEE Trans. Knowl. Data Eng., 2016

Impact of Surface Water Layers on Protein-Ligand Binding: How Well Are Experimental Data Reproduced by Molecular Dynamics Simulations in a Thermolysin Test Case?
Journal of Chemical Information and Modeling, 2016

2015
Large-Scale Mining for Similar Protein Binding Pockets: With RAPMAD Retrieval on the Fly Becomes Real.
Journal of Chemical Information and Modeling, 2015

Thermodynamics of protein-ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data.
Journal of Computer-Aided Molecular Design, 2015

2014
Identification of Functionally Related Enzymes by Learning-to-Rank Methods.
IEEE/ACM Trans. Comput. Biology Bioinform., 2014

Extended Graph-Based Models for Enhanced Similarity Search in Cavbase.
IEEE/ACM Trans. Comput. Biology Bioinform., 2014

Extraction of Protein Binding Pockets in Close Neighborhood of Bound Ligands Makes Comparisons Simple Due to Inherent Shape Similarity.
Journal of Chemical Information and Modeling, 2014

A new method for rapid comparison of protein binding pockets by capturing spatial distributions.
J. Cheminformatics, 2014

Identification of functionally related enzymes by learning-to-rank methods.
CoRR, 2014

2013
Local Clique Merging: An Extension of the Maximum Common Subgraph Measure with Applications in Structural Bioinformatics.
Proceedings of the Algorithms from and for Nature and Life, 2013

Graph-based methods for protein structure comparison.
Wiley Interdisc. Rew.: Data Mining and Knowledge Discovery, 2013

Cavities Tell More than Sequences: Exploring Functional Relationships of Proteases via Binding Pockets.
Journal of Chemical Information and Modeling, 2013

Extended graph-based models for enhanced similarity retrieval in Cavbase.
J. Cheminformatics, 2013

2011
SEGA: Semiglobal Graph Alignment for Structure-Based Protein Comparison.
IEEE/ACM Trans. Comput. Biology Bioinform., 2011

Superposition and Alignment of Labeled Point Clouds.
IEEE/ACM Trans. Comput. Biology Bioinform., 2011

MiniMuDS: A New Optimizer using Knowledge-Based Potentials Improves Scoring of Docking Solutions.
Journal of Chemical Information and Modeling, 2011

DSX: A Knowledge-Based Scoring Function for the Assessment of Protein-Ligand Complexes.
Journal of Chemical Information and Modeling, 2011

On the validity of popular assumptions in computational drug design.
J. Cheminformatics, 2011

LigpKa - a database of pKa values for small molecule ligands designed for the use in structure-based pKa calculations.
J. Cheminformatics, 2011

fconv: format conversion, manipulation and feature computation of molecular data.
Bioinformatics, 2011

2010
GARLig: A Fully Automated Tool for Subset Selection of Large Fragment Spaces via a Self-Adaptive Genetic Algorithm.
Journal of Chemical Information and Modeling, 2010

Efficient Similarity Retrieval of Protein Binding Sites based on Histogram Comparison.
Proceedings of the German Conference on Bioinformatics 2010, 2010

2009
Secbase: Database Module To Retrieve Secondary Structure Elements with Ligand Binding Motifs.
Journal of Chemical Information and Modeling, 2009

Molecular Docking Screens Using Comparative Models of Proteins.
Journal of Chemical Information and Modeling, 2009

Evolutionary construction of multiple graph alignments for the structural analysis of biomolecules.
Bioinformatics, 2009

Efficient Construction of Multiple Geometrical Alignments for the Comparison of Protein Binding Sites.
Proceedings of the Ninth International Conference on Intelligent Systems Design and Applications, 2009

2008
Use of 3D QSAR Models for Database Screening: A Feasibility Study.
Journal of Chemical Information and Modeling, 2008

2007
Multiple Graph Alignment for the Structural Analysis of Protein Active Sites.
IEEE/ACM Trans. Comput. Biology Bioinform., 2007

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations.
Nucleic Acids Research, 2007

Atypical Protonation States in the Active Site of HIV-1 Protease: A Computational Study.
Journal of Chemical Information and Modeling, 2007

Graph Alignment: Fuzzy Pattern Mining for the Structural Analysis of Protein Active Sites.
Proceedings of the FUZZ-IEEE 2007, 2007

2006
AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB.
Nucleic Acids Research, 2006

3D QSAR Selectivity Analyses of Carbonic Anhydrase Inhibitors: Insights for the Design of Isozyme Selective Inhibitors.
Journal of Chemical Information and Modeling, 2006

2004
Comparison of substructural epitopes in enzyme active sites using self-organizing maps.
Journal of Computer-Aided Molecular Design, 2004

Efficient similarity search in protein structure databases by k-clique hashing.
Bioinformatics, 2004

Graph Alignments: A New Concept to Detect Conserved Regions in Protein Active Sites.
Proceedings of the German Conference on Bioinformatics (GCB 2004), Bielefeld, 2004

2003
A 3D QSAR Study on a Set of Dopamine D4 Receptor Antagonists.
Journal of Chemical Information and Computer Sciences, 2003

Efficient Similarity Search in Protein Structure Databases: Improving Cliqae-Detection through Clique Hashing.
Proceedings of the German Conference on Bioinformatics, 2003

2000
Simple knowledge-based descriptors to predict protein-ligand interactions. Methodology and validation.
Journal of Computer-Aided Molecular Design, 2000

1999
Methodological developments and strategies for a fast flexible superposition of drug-size molecules.
Journal of Computer-Aided Molecular Design, 1999

Comparative Molecular Similarity Index Analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries.
Journal of Computer-Aided Molecular Design, 1999

1997
Superposition of molecules: Electron density fitting by application of fourier transforms.
Journal of Computational Chemistry, 1997

1996
A Systemsatic Approach to Finding New Lead Structures Having Biological Activity.
Proceedings of the Bioinformatics, German Conference on Bioinformatics, Leipzig, 1996

1994
Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures.
Journal of Chemical Information and Computer Sciences, 1994

Different approaches toward an automatic structural alignment of drug moleculars: Applications to sterol mimics, thrombin and thermolysin inhibitors.
Journal of Computer-Aided Molecular Design, 1994

A fast and efficient method to generate biologically relevant conformations.
Journal of Computer-Aided Molecular Design, 1994

1989
Durch die Berechnung von Moleküleigenschaften zum gezielten Entwurf von neuen Wirkstoffen.
Proceedings of the Supercomputer'89: Anwendungen, Architekturen, Trends, 1989


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