List of works - Gerhard Klebe

A Small Nonrule of 3 Compatible Fragment Library Provides High Hit Rate of Endothiapepsin Crystal Structures with Various Fragment Chemotypes ⬇️

scientific article published on October 25, 2011

A Structure-Based Approach to Ligand Discovery for 2 C -Methyl- d -erythritol-2,4-cyclodiphosphate Synthase: A Target for Antimicrobial Therapy †

scientific article

Achiral oligoamines as versatile tool for the development of aspartic protease inhibitors

scientific article

AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB

scientific article

An essential role for aspartate 264 in catalysis by tRNA-guanine transglycosylase from Escherichia coli

scientific article

An integrative approach combining noncovalent mass spectrometry, enzyme kinetics and X-ray crystallography to decipher Tgt protein-protein and protein-RNA interaction

scientific article

Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

scientific article (publication date: 2 August 2002)

Beyond Heparinization: Design of Highly Potent Thrombin Inhibitors Suitable for Surface Coupling ⬇️

scientific article published on August 20, 2012

Beyond affinity: enthalpy-entropy factorization unravels complexity of a flat structure-activity relationship for inhibition of a tRNA-modifying enzyme

scientific article

Bidentate Zinc Chelators for α-Carbonic Anhydrases that Produce a Trigonal Bipyramidal Coordination Geometry

scientific article

Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures

scientific article

Chasing protons: how isothermal titration calorimetry, mutagenesis, and pKa calculations trace the locus of charge in ligand binding to a tRNA-binding enzyme

scientific article

Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures

scientific article (publication date: July 1994)

Congeneric but Still Distinct: How Closely Related Trypsin Ligands Exhibit Different Thermodynamic and Structural Properties ⬇️

scientific article published on November 25, 2010

Crystal Structure of 2-Methylisocitrate Lyase (PrpB) from Escherichia coli and Modelling of its Ligand Bound Active Centre ⬇️

scientific article (publication date: 2 May 2003)

Crystal structure analysis and in silico pKa calculations suggest strong pKa shifts of ligands as driving force for high-affinity binding to TGT

scientific article

Crystal structure of Bacillus subtilis S-adenosylmethionine:tRNA ribosyltransferase-isomerase

scientific article

Crystal structures of tRNA-guanine transglycosylase (TGT) in complex with novel and potent inhibitors unravel pronounced induced-fit adaptations and suggest dimer formation upon substrate binding

scientific article

De novo design, synthesis, and in vitro evaluation of inhibitors for prokaryotic tRNA-guanine transglycosylase: a dramatic sulfur effect on binding affinity

scientific article

Dissecting the Hydrophobic Effect on the Molecular Level: The Role of Water, Enthalpy, and Entropy in Ligand Binding to Thermolysin ⬇️

scientific article published on January 2, 2013

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

scientific article

Evidence for a novel binding site conformer of aldose reductase in ligand-bound state

scientific article

Experimental and Computational Active Site Mapping as a Starting Point to Fragment‐Based Lead Discovery ⬇️

scientific article published on December 23, 2011

Fingerprint Kernels for Protein Structure Comparison

scientific article

Flexible adaptations in the structure of the tRNA-modifying enzyme tRNA-guanine transglycosylase and their implications for substrate selectivity, reaction mechanism and structure-based drug design

scientific article

Fragment Binding Can Be Either More Enthalpy-Driven or Entropy-Driven: Crystal Structures and Residual Hydration Patterns Suggest Why

scientific article

Fragment-based lead discovery: screening and optimizing fragments for thermolysin inhibition

scientific article

From lin-benzoguanines to lin-benzohypoxanthines as ligands for Zymomonas mobilis tRNA-guanine transglycosylase: replacement of protein-ligand hydrogen bonding by importing water clusters

scientific article

Glutamate versus Glutamine Exchange Swaps Substrate Selectivity in tRNA-Guanine Transglycosylase: Insight into the Regulation of Substrate Selectivity by Kinetic and Crystallographic Studies

scientific article

High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits

scientific article

Hot-spot analysis to dissect the functional protein-protein interface of a tRNA-modifying enzyme

scientific article

How to replace the residual solvation shell of polar active site residues to achieve nanomolar inhibition of tRNA-guanine transglycosylase

scientific article

Identification of a novel polyfluorinated compound as a lead to inhibit the human enzymes aldose reductase and AKR1B10: structure determination of both ternary complexes and implications for drug design

scientific article

Identification of novel aldose reductase inhibitors based on carboxymethylated mercaptotriazinoindole scaffold

scientific article

Investigation of Specificity Determinants in Bacterial tRNA-Guanine Transglycosylase Reveals Queuine, the Substrate of Its Eucaryotic Counterpart, as Inhibitor ⬇️

scientific article published on May 21, 2013

KNOBLE: a knowledge-based approach for the design and synthesis of readily accessible small-molecule chemical probes to test protein binding

scientific article

Kinetic and Structural Insights into the Mechanism of Binding of Sulfonamides to Human Carbonic Anhydrase by Computational and Experimental Studies

scientific article

Ligand Binding Stepwise Disrupts Water Network in Thrombin: Enthalpic and Entropic Changes Reveal Classical Hydrophobic Effect ⬇️

scientific article published on June 25, 2012

Ligand-induced fit affects binding modes and provokes changes in crystal packing of aldose reductase ⬇️

scientific article published on June 13, 2011

Merging the binding sites of aldose and aldehyde reductase for detection of inhibitor selectivity-determining features

scientific article

Methyl, ethyl, propyl, butyl: futile but not for water, as the correlation of structure and thermodynamic signature shows in a congeneric series of thermolysin inhibitors

scientific article

New Insights into Human 17β-Hydroxysteroid Dehydrogenase Type 14: First Crystal Structures in Complex with a Steroidal Ligand and with a Potent Nonsteroidal Inhibitor

scientific article

Non-additivity of functional group contributions in protein-ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry

scientific article

Occupying a flat subpocket in a tRNA-modifying enzyme with ordered or disordered side chains: Favorable or unfavorable for binding?

scientific article

Optimization of Cyclic Plasmin Inhibitors: From Benzamidines to Benzylamines

scientific article

Potent inhibitors of tRNA-guanine transglycosylase, an enzyme linked to the pathogenicity of the Shigella bacterium: charge-assisted hydrogen bonding

scientific article published in 2007

Prediction of turn types in protein structure by machine-learning classifiers.

scientific article

Radiation damage reveals promising interaction position

scientific article

Reconstructing the binding site of factor Xa in trypsin reveals ligand-induced structural plasticity

scientific article

Replacement of water molecules in a phosphate binding site by furanoside-appended lin-benzoguanine ligands of tRNA-guanine transglycosylase (TGT)

scientific article

Saccharin inhibits carbonic anhydrases: possible explanation for its unpleasant metallic aftertaste

scientific article

Stereo‐ and Regioselective Azide/Alkyne Cycloadditions in Carbonic Anhydrase II via Tethering, Monitored by Crystallography and Mass Spectrometry ⬇️

scientific article published on April 19, 2011

Structural Determinants of the Selectivity of 3-Benzyluracil-1-acetic Acids toward Human Enzymes Aldose Reductase and AKR1B10

scientific article

Structural and kinetic analysis of pyrrolidine-based inhibitors of the drug-resistant Ile84Val mutant of HIV-1 protease

scientific article

Structural and thermodynamic study on aldose reductase: nitro-substituted inhibitors with strong enthalpic binding contribution

scientific article

Structure and substrate docking of a hydroxy(phenyl)pyruvate reductase from the higher plant Coleus blumei Benth

scientific article

Structure of active coagulation factor XIII triggered by calcium binding: basis for the design of next-generation anticoagulants

scientific article

Structure-based design of inhibitors of the aspartic protease endothiapepsin by exploiting dynamic combinatorial chemistry

scientific article

Structure-based optimization of aldose reductase inhibitors originating from virtual screening

scientific article

Structure-guided design of C2-symmetric HIV-1 protease inhibitors based on a pyrrolidine scaffold

scientific article

Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation

scientific article

Targeting the open-flap conformation of HIV-1 protease with pyrrolidine-based inhibitors

scientific article

The crystal structure of Plasmodium falciparum glutamate dehydrogenase, a putative target for novel antimalarial drugs

scientific article

Thermodynamic inhibition profile of a cyclopentyl and a cyclohexyl derivative towards thrombin: the same but for different reasons

scientific article

Thermodynamics of protein-ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data

scientific article

Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin

scientific article

Tracing binding modes in hit-to-lead optimization: chameleon-like poses of aspartic protease inhibitors

scientific article

Tracing the Detail: How Mutations Affect Binding Modes and Thermodynamic Signatures of Closely Related Aldose Reductase Inhibitors ⬇️

scientific article published on December 23, 2010

Two Solutions for the Same Problem: Multiple Binding Modes of Pyrrolidine-Based HIV-1 Protease Inhibitors ⬇️

scientific article published on July 22, 2011

Understanding binding selectivity toward trypsin and factor Xa: the role of aromatic interactions

scientific article

Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: new pharmacological opportunities due to related binding site recognition

scientific article

Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis

scientific article (publication date: 27 March 2003)

Water makes the difference: rearrangement of water solvation layer triggers non-additivity of functional group contributions in protein-ligand binding

scientific article

pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design

scientific article

List of works by Gerhard Klebe

A Small Nonrule of 3 Compatible Fragment Library Provides High Hit Rate of Endothiapepsin Crystal Structures with Various Fragment Chemotypes ⬇️

A Structure-Based Approach to Ligand Discovery for 2 C -Methyl- d -erythritol-2,4-cyclodiphosphate Synthase: A Target for Antimicrobial Therapy †

Achiral oligoamines as versatile tool for the development of aspartic protease inhibitors

AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB

An essential role for aspartate 264 in catalysis by tRNA-guanine transglycosylase from Escherichia coli

An integrative approach combining noncovalent mass spectrometry, enzyme kinetics and X-ray crystallography to decipher Tgt protein-protein and protein-RNA interaction

Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

Beyond Heparinization: Design of Highly Potent Thrombin Inhibitors Suitable for Surface Coupling ⬇️

Beyond affinity: enthalpy-entropy factorization unravels complexity of a flat structure-activity relationship for inhibition of a tRNA-modifying enzyme

Bidentate Zinc Chelators for α-Carbonic Anhydrases that Produce a Trigonal Bipyramidal Coordination Geometry

Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures

Chasing protons: how isothermal titration calorimetry, mutagenesis, and pKa calculations trace the locus of charge in ligand binding to a tRNA-binding enzyme

Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures

Congeneric but Still Distinct: How Closely Related Trypsin Ligands Exhibit Different Thermodynamic and Structural Properties ⬇️

Crystal Structure of 2-Methylisocitrate Lyase (PrpB) from Escherichia coli and Modelling of its Ligand Bound Active Centre ⬇️

Crystal structure analysis and in silico pKa calculations suggest strong pKa shifts of ligands as driving force for high-affinity binding to TGT

Crystal structure of Bacillus subtilis S-adenosylmethionine:tRNA ribosyltransferase-isomerase

Crystal structures of tRNA-guanine transglycosylase (TGT) in complex with novel and potent inhibitors unravel pronounced induced-fit adaptations and suggest dimer formation upon substrate binding

De novo design, synthesis, and in vitro evaluation of inhibitors for prokaryotic tRNA-guanine transglycosylase: a dramatic sulfur effect on binding affinity

Dissecting the Hydrophobic Effect on the Molecular Level: The Role of Water, Enthalpy, and Entropy in Ligand Binding to Thermolysin ⬇️

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

Evidence for a novel binding site conformer of aldose reductase in ligand-bound state

Experimental and Computational Active Site Mapping as a Starting Point to Fragment‐Based Lead Discovery ⬇️

Fingerprint Kernels for Protein Structure Comparison

Flexible adaptations in the structure of the tRNA-modifying enzyme tRNA-guanine transglycosylase and their implications for substrate selectivity, reaction mechanism and structure-based drug design

Fragment Binding Can Be Either More Enthalpy-Driven or Entropy-Driven: Crystal Structures and Residual Hydration Patterns Suggest Why

Fragment-based lead discovery: screening and optimizing fragments for thermolysin inhibition

From lin-benzoguanines to lin-benzohypoxanthines as ligands for Zymomonas mobilis tRNA-guanine transglycosylase: replacement of protein-ligand hydrogen bonding by importing water clusters

Glutamate versus Glutamine Exchange Swaps Substrate Selectivity in tRNA-Guanine Transglycosylase: Insight into the Regulation of Substrate Selectivity by Kinetic and Crystallographic Studies

High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits

Hot-spot analysis to dissect the functional protein-protein interface of a tRNA-modifying enzyme

How to replace the residual solvation shell of polar active site residues to achieve nanomolar inhibition of tRNA-guanine transglycosylase

Identification of a novel polyfluorinated compound as a lead to inhibit the human enzymes aldose reductase and AKR1B10: structure determination of both ternary complexes and implications for drug design

Identification of novel aldose reductase inhibitors based on carboxymethylated mercaptotriazinoindole scaffold

Investigation of Specificity Determinants in Bacterial tRNA-Guanine Transglycosylase Reveals Queuine, the Substrate of Its Eucaryotic Counterpart, as Inhibitor ⬇️

KNOBLE: a knowledge-based approach for the design and synthesis of readily accessible small-molecule chemical probes to test protein binding

Kinetic and Structural Insights into the Mechanism of Binding of Sulfonamides to Human Carbonic Anhydrase by Computational and Experimental Studies

Ligand Binding Stepwise Disrupts Water Network in Thrombin: Enthalpic and Entropic Changes Reveal Classical Hydrophobic Effect ⬇️

Ligand-induced fit affects binding modes and provokes changes in crystal packing of aldose reductase ⬇️

Merging the binding sites of aldose and aldehyde reductase for detection of inhibitor selectivity-determining features

Methyl, ethyl, propyl, butyl: futile but not for water, as the correlation of structure and thermodynamic signature shows in a congeneric series of thermolysin inhibitors

New Insights into Human 17β-Hydroxysteroid Dehydrogenase Type 14: First Crystal Structures in Complex with a Steroidal Ligand and with a Potent Nonsteroidal Inhibitor

Non-additivity of functional group contributions in protein-ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry

Occupying a flat subpocket in a tRNA-modifying enzyme with ordered or disordered side chains: Favorable or unfavorable for binding?

Optimization of Cyclic Plasmin Inhibitors: From Benzamidines to Benzylamines

Potent inhibitors of tRNA-guanine transglycosylase, an enzyme linked to the pathogenicity of the Shigella bacterium: charge-assisted hydrogen bonding

Prediction of turn types in protein structure by machine-learning classifiers.

Radiation damage reveals promising interaction position

Reconstructing the binding site of factor Xa in trypsin reveals ligand-induced structural plasticity

Replacement of water molecules in a phosphate binding site by furanoside-appended lin-benzoguanine ligands of tRNA-guanine transglycosylase (TGT)

Saccharin inhibits carbonic anhydrases: possible explanation for its unpleasant metallic aftertaste

Stereo‐ and Regioselective Azide/Alkyne Cycloadditions in Carbonic Anhydrase II via Tethering, Monitored by Crystallography and Mass Spectrometry ⬇️

Structural Determinants of the Selectivity of 3-Benzyluracil-1-acetic Acids toward Human Enzymes Aldose Reductase and AKR1B10

Structural and kinetic analysis of pyrrolidine-based inhibitors of the drug-resistant Ile84Val mutant of HIV-1 protease

Structural and thermodynamic study on aldose reductase: nitro-substituted inhibitors with strong enthalpic binding contribution

Structure and substrate docking of a hydroxy(phenyl)pyruvate reductase from the higher plant Coleus blumei Benth

Structure of active coagulation factor XIII triggered by calcium binding: basis for the design of next-generation anticoagulants

Structure-based design of inhibitors of the aspartic protease endothiapepsin by exploiting dynamic combinatorial chemistry

Structure-based optimization of aldose reductase inhibitors originating from virtual screening

Structure-guided design of C2-symmetric HIV-1 protease inhibitors based on a pyrrolidine scaffold

Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation

Targeting the open-flap conformation of HIV-1 protease with pyrrolidine-based inhibitors

The crystal structure of Plasmodium falciparum glutamate dehydrogenase, a putative target for novel antimalarial drugs

Thermodynamic inhibition profile of a cyclopentyl and a cyclohexyl derivative towards thrombin: the same but for different reasons

Thermodynamics of protein-ligand interactions as a reference for computational analysis: how to assess accuracy, reliability and relevance of experimental data

Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin

Tracing binding modes in hit-to-lead optimization: chameleon-like poses of aspartic protease inhibitors

Tracing the Detail: How Mutations Affect Binding Modes and Thermodynamic Signatures of Closely Related Aldose Reductase Inhibitors ⬇️

Two Solutions for the Same Problem: Multiple Binding Modes of Pyrrolidine-Based HIV-1 Protease Inhibitors ⬇️

Understanding binding selectivity toward trypsin and factor Xa: the role of aromatic interactions

Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: new pharmacological opportunities due to related binding site recognition

Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis

Water makes the difference: rearrangement of water solvation layer triggers non-additivity of functional group contributions in protein-ligand binding

pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design