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Gerhard Klebe

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Florian C Schrader; Gustavo A Afanador; Hans-Martin Dahse; Serghei Glinca; Gerhard Klebe; Michael Lanzer; Ann-Kristin Mueller; Sean T Prigge; Julia M Sattler; Martin Schlitzer
Novel type II fatty acid biosynthesis (FAS II) inhibitors as multistage antimalarial agents.
Sebastian M Saupe; Michael Betz; Gerhard Klebe; Stephanie Leubner; Torsten Steinmetzer
Development of new cyclic plasmin inhibitors with excellent potency and selectivity.
Alexander Biela; David Hangauer; Andreas Heine; Michael Betz; Nader N Nasief; Gerhard Klebe
Dissecting the hydrophobic effect on the molecular level: the role of water, enthalpy, and entropy in ligand binding to thermolysin.

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All Publications

2013: Florian C Schrader; Gustavo A Afanador; Hans-Martin Dahse; Serghei Glinca; Gerhard Klebe; Michael Lanzer; Ann-Kristin Mueller; Sean T Prigge; Julia M Sattler; Martin Schlitzer
Novel type II fatty acid biosynthesis (FAS II) inhibitors as multistage antimalarial agents.
ChemMedChem 2013;8(3):442-61.
2013: Sebastian M Saupe; Michael Betz; Gerhard Klebe; Stephanie Leubner; Torsten Steinmetzer
Development of new cyclic plasmin inhibitors with excellent potency and selectivity.
Journal of medicinal chemistry 2013;56(3):820-31.
2013: Alexander Biela; David Hangauer; Andreas Heine; Michael Betz; Nader N Nasief; Gerhard Klebe
Dissecting the hydrophobic effect on the molecular level: the role of water, enthalpy, and entropy in ligand binding to thermolysin.
Angewandte Chemie (International ed. in English) 2013;52(6):1822-8.
2013: Olga Samsonova; Gerhard Klebe; Christian Pfeiffer; Damla Sahin; Adam Biela; Eyas Dayyoub; Serghei Glinca; Thomas Kissel
The use of isothermal titration calorimetry and molecular dynamics to show variability in DNA transfection performance.
Acta biomaterialia 2013;9(2):4994-5002.
2013: Inna Biela; Hans-Dieter Gerber; Serghei Glinca; Andreas Heine; Florian Immekus; Gerhard Klebe; Tran Xuan Phong Nguyen; Naomi Tidten-Luksch; Klaus Reuter
Investigation of Specificity Determinants in Bacterial tRNA-Guanine Transglycosylase Reveals Queuine, the Substrate of Its Eucaryotic Counterpart, as Inhibitor.
PloS one 2013;8(5):e64240.
2012: Mengyao Zheng; Andrea Danani; Gerhard Klebe; Olivia Merkel; Manuel Neeb; Giovanni M Pavan; Andreas K Schaper; Thomas Kissel
Targeting the blind spot of polycationic nanocarrier-based siRNA delivery.
ACS nano 2012;6(11):9447-54.
2012: Hans-Dieter Gerber; Gerhard Klebe
Concise and efficient syntheses of preQ1 base, Q base, and (ent)-Q base.
Organic & biomolecular chemistry 2012;10(43):8660-8.
2012: Regina Reul; Udo Bakowsky; Adam Biela; Gerhard Klebe; Elena Marxer; Juliane Nguyen; Thomas Kissel
Biophysical and biological investigation of DNA nano-complexes with a non-toxic, biodegradable amine-modified hyperbranched polyester.
International journal of pharmaceutics 2012;436(1-2):97-105.
2012: Dragana Cubrilovic; Gerhard Klebe; Frank Sielaff; Torsten Steinmetzer; Adam Biela; Renato Zenobi
Quantifying protein-ligand binding constants using electrospray ionization mass spectrometry: a systematic binding affinity study of a series of hydrophobically modified trypsin inhibitors.
Journal of the American Society for Mass Spectrometry 2012;23(10):1768-77.
2012: Alexander Biela; Andreas Heine; Michael Betz; Gerhard Klebe
Water makes the difference: rearrangement of water solvation layer triggers non-additivity of functional group contributions in protein-ligand binding.
ChemMedChem 2012;7(8):1423-34.
2012: Luzi Jakob Barandun; Andreas Heine; Florian Immekus; Manfred Kansy; Gerhard Klebe; Philipp C Kohler; Tina Ritschel; Sandro Tonazzi; Björn Wagner; Severin Wendelspiess; François Diederich
From lin-benzoguanines to lin-benzohypoxanthines as ligands for Zymomonas mobilis tRNA-guanine transglycosylase: replacement of protein-ligand hydrogen bonding by importing water clusters.
Chemistry (Weinheim an der Bergstrasse, Germany) 2012;18(30):9246-57.
2012: Adam Biela; Andreas Heine; Frank Sielaff; Torsten Steinmetzer; Felix Terwesten; Gerhard Klebe
Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect.
Journal of medicinal chemistry 2012;55(13):6094-110.
2012: Alexander Biela; D Hangauer; Andreas Heine; M Khayat; J Kong; H Tan; Gerhard Klebe
Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin.
Journal of molecular biology 2012;418(5):350-66.
2012: Jürgen Behnen; Tobias Craan; Andreas Heine; Helene Köster; Gerd Neudert; Gerhard Klebe
Experimental and computational active site mapping as a starting point to fragment-based lead discovery.
ChemMedChem 2012;7(2):248-61.
2011: Peter Kolb; Gerhard Klebe
The golden age of GPCR structural biology: any impact on drug design?
Angewandte Chemie (International ed. in English) 2011;50(49):11573-5.
2011: Helene Köster; Lars Neumann; Matthias Zentgraf; Sascha Brass; Tobias Craan; Andreas Heine; Christian Herhaus; Gerhard Klebe
A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes.
Journal of medicinal chemistry 2011;54(22):7784-96.
2011: Simone Naruhn; Veronika Pape; Philipp M Toth; Sabine Müller-Brüsselbach; Till Adhikary; Wibke E Diederich; Stefanie Dörr; Kerstin Kaddatz; Gerhard Klebe; Rolf Mueller
High-affinity peroxisome proliferator-activated receptor β/δ-specific ligands with pure antagonistic or inverse agonistic properties.
Molecular pharmacology 2011;80(5):828-38.
2011: Thomas Fober; Serghei Glinca; Gerhard Klebe; Eyke Hüllermeier
Superposition and alignment of labeled point clouds.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2011;8(6):1653-66.
2011: Gerd Neudert; Gerhard Klebe
DSX: a knowledge-based scoring function for the assessment of protein-ligand complexes.
Journal of chemical information and modeling 2011;51(10):2731-45.
2011: Cornelia Koch; Andreas Heine; Gerhard Klebe
Radiation damage reveals promising interaction position.
Journal of synchrotron radiation 2011;18(Pt 5):782-9.
2011: Marco Mernberger; Gerhard Klebe; Eyke Hüllermeier
SEGA: semiglobal graph alignment for structure-based protein comparison.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2011;8(5):1330-43.
2011: Andreas Blum; Jark Böttcher; Stefanie Dörr; Andreas Heine; Gerhard Klebe; Wibke E Diederich
Two solutions for the same problem: multiple binding modes of pyrrolidine-based HIV-1 protease inhibitors.
Journal of molecular biology 2011;410(4):745-55.
2011: Andreas Spitzmüller; Hans F G Velec; Gerhard Klebe
MiniMuDS: a new optimizer using knowledge-based potentials improves scoring of docking solutions.
Journal of chemical information and modeling 2011;51(6):1423-30.
2011: Johannes Schulze Wischeler; Dong Sun; Nicola U Sandner; Uwe Linne; Andreas Heine; Ulrich Koert; Gerhard Klebe
Stereo- and regioselective azide/alkyne cycloadditions in carbonic anhydrase II via tethering, monitored by crystallography and mass spectrometry.
Chemistry (Weinheim an der Bergstrasse, Germany) 2011;17(21):5842-51.
2011: Gerd Neudert; Gerhard Klebe
fconv: Format conversion, manipulation and feature computation of molecular data.
Bioinformatics (Oxford, England) 2011;27(7):1021-2.
2011: Gerhard Klebe; Martin Schlitzer
[M2 inhibitors and neuraminidase inhibitors].
Pharmazie in unserer Zeit 2011;40(2):144-50.
2011: Tobias Brandt; Nicole Holzmann; Laveena Muley; Maan Khayat; Christof Wegscheid-Gerlach; Bernhard Baum; Andreas Heine; David Hangauer; Gerhard Klebe
Congeneric but still distinct: how closely related trypsin ligands exhibit different thermodynamic and structural properties.
Journal of molecular biology 2011;405(5):1170-87.
2010: L Englert; Alexander Biela; M Zayed; Andreas Heine; D Hangauer; Gerhard Klebe
Displacement of disordered water molecules from hydrophobic pocket creates enthalpic signature: binding of phosphonamidate to the S₁'-pocket of thermolysin.
Biochimica et biophysica acta 2010;1800(11):1192-202.
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.
Journal of chemical information and modeling 2010;50(9):1644-59.
2010: Johannes Schulze Wischeler; Alessio Innocenti; Daniela Vullo; Arpita Agrawal; Seth M Cohen; Andreas Heine; Claudiu T Supuran; Gerhard Klebe
Bidentate Zinc chelators for alpha-carbonic anhydrases that produce a trigonal bipyramidal coordination geometry.
ChemMedChem 2010;5(9):1609-15.
2010: Lisa Englert; Katrin Silber; Holger Steuber; Sascha Brass; Björn Over; Hans-Dieter Gerber; Andreas Heine; Wibke E Diederich; Gerhard Klebe
Fragment-based lead discovery: screening and optimizing fragments for thermolysin inhibition.
ChemMedChem 2010;5(6):930-40.
2010: Verena Janiak; Maike Petersen; Matthias Zentgraf; Gerhard Klebe; Andreas Heine
Structure and substrate docking of a hydroxy(phenyl)pyruvate reductase from the higher plant Coleus blumei Benth.
Acta crystallographica. Section D, Biological crystallography 2010;66(Pt 5):593-603.
2010: Bernhard Baum; Laveena Muley; Michael Smolinski; Andreas Heine; David Hangauer; Gerhard Klebe
Non-additivity of functional group contributions in protein-ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry.
Journal of molecular biology 2010;397(4):1042-54.
2010: Torsten Luksch; Andreas Blum; Nina Klee; Wibke E Diederich; Christoph A Sotriffer; Gerhard Klebe
Pyrrolidine derivatives as plasmepsin inhibitors: binding mode analysis assisted by molecular dynamics simulations of a highly flexible protein.
ChemMedChem 2010;5(3):443-54.
2009: Tina Ritschel; Philipp C Kohler; Gerd Neudert; Andreas Heine; François Diederich; Gerhard Klebe
How to replace the residual solvation shell of polar active site residues to achieve nanomolar inhibition of tRNA-guanine transglycosylase.
ChemMedChem 2009;4(12):2012-23.
2009: Tina Ritschel; Cédric Atmanene; Klaus Reuter; Alain Van Dorsselaer; Sarah Sanglier-Cianferani; Gerhard Klebe
An integrative approach combining noncovalent mass spectrometry, enzyme kinetics and X-ray crystallography to decipher Tgt protein-protein and protein-RNA interaction.
Journal of molecular biology 2009;393(4):833-47.
2009: Hao Fan; John J Irwin; Benjamin M Webb; Gerhard Klebe; Brian K Shoichet; Andrej Sali
Molecular docking screens using comparative models of proteins.
Journal of chemical information and modeling 2009;49(11):2512-27.
2009: Philipp C Kohler; Tina Ritschel; W Bernd Schweizer; Gerhard Klebe; François Diederich
High-affinity inhibitors of tRNA-guanine transglycosylase replacing the function of a structural water cluster.
Chemistry (Weinheim an der Bergstrasse, Germany) 2009;15(41):10809-17.
2009: Bernhard Baum; Laveena Muley; Andreas Heine; Michael Smolinski; David Hangauer; Gerhard Klebe
Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin.
Journal of molecular biology 2009;391(3):552-64.
2009: Thomas Fober; Marco Mernberger; Gerhard Klebe; Eyke Hüllermeier
Evolutionary construction of multiple graph alignments for the structural analysis of biomolecules.
Bioinformatics (Oxford, England) 2009;25(16):2110-7.
2009: Nils Weskamp; Eyke Hüllermeier; Gerhard Klebe
Merging chemical and biological space: Structural mapping of enzyme binding pocket space.
Proteins 2009;76(2):317-30.
2009: Bernhard Baum; Menshawy Mohamed; Mohamed Zayed; Christof Gerlach; Andreas Heine; David Hangauer; Gerhard Klebe
More than a simple lipophilic contact: a detailed thermodynamic analysis of nonbasic residues in the s1 pocket of thrombin.
Journal of molecular biology 2009;390(1):56-69.
2009: Michael Eisenmann; Holger Steuber; Matthias Zentgraf; Mirko Altenkämper; Regina Ortmann; Johann Perruchon; Gerhard Klebe; Martin Schlitzer
Structure-based optimization of aldose reductase inhibitors originating from virtual screening.
ChemMedChem 2009;4(5):809-19.
2009: Nicola L Ramsden; Lori Buetow; Alice Dawson; Lauris A Kemp; Venkatsubramanian Ulaganathan; Ruth Brenk; Gerhard Klebe; William N Hunter
A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy.
Journal of medicinal chemistry 2009;52(8):2531-42.
2009: Tina Ritschel; Simone Hoertner; Andreas Heine; François Diederich; Gerhard Klebe
Crystal structure analysis and in silico pKa calculations suggest strong pKa shifts of ligands as driving force for high-affinity binding to TGT.
Chembiochem : a European journal of chemical biology 2009;10(4):716-27.
2008: Jark Böttcher; Andreas Blum; Andreas Heine; Wibke E Diederich; Gerhard Klebe
Structural and kinetic analysis of pyrrolidine-based inhibitors of the drug-resistant Ile84Val mutant of HIV-1 protease.
Journal of molecular biology 2008;383(2):347-57.
2008: Christoph A Sotriffer; Paul Sanschagrin; Hans Matter; Gerhard Klebe
SFCscore: scoring functions for affinity prediction of protein-ligand complexes.
Proteins 2008;73(2):395-419.
2008: Andreas Blum; Jark Böttcher; Benedikt Sammet; Torsten Luksch; Andreas Heine; Gerhard Klebe; Wibke E Diederich
Achiral oligoamines as versatile tool for the development of aspartic protease inhibitors.
Bioorganic & medicinal chemistry 2008;16(18):8574-86.
2008: Torsten Luksch; Nan-Si Chan; Sascha Brass; Christoph A Sotriffer; Gerhard Klebe; Wibke E Diederich
Computer-aided design and synthesis of nonpeptidic plasmepsin II and IV inhibitors.
ChemMedChem 2008;3(9):1323-36.
2008: Jark Böttcher; Andreas Blum; Stefanie Dörr; Andreas Heine; Wibke E Diederich; Gerhard Klebe
Targeting the open-flap conformation of HIV-1 protease with pyrrolidine-based inhibitors.
ChemMedChem 2008;3(9):1337-44.
2008: Katja Kohring; Jochen Wiesner; Mirko Altenkämper; Jacek Sakowski; Katrin Silber; Alexander Hillebrecht; Peter Haebel; Hans-Martin Dahse; Regina Ortmann; Hassan Jomaa; Gerhard Klebe; Martin Schlitzer
Development of benzophenone-based farnesyltransferase inhibitors as novel antimalarials.
ChemMedChem 2008;3(8):1217-31.
2008: Johann Perruchon; Regina Ortmann; Mirko Altenkämper; Katrin Silber; Jochen Wiesner; Hassan Jomaa; Gerhard Klebe; Martin Schlitzer
Studies addressing the importance of charge in the binding of fosmidomycin-like molecules to deoxyxylulosephosphate reductoisomerase.
ChemMedChem 2008;3(8):1232-41.
2008: Holger Steuber; Andreas Heine; alberto podjarny; Gerhard Klebe
Merging the binding sites of aldose and aldehyde reductase for detection of inhibitor selectivity-determining features.
Journal of molecular biology 2008;379(5):991-1016.
2008: Katrin Kupas; Alfred Ultsch; Gerhard Klebe
Large scale analysis of protein-binding cavities using self-organizing maps and wavelet-based surface patches to describe functional properties, selectivity discrimination, and putative cross-reactivity.
Proteins 2008;71(3):1288-306.
2008: Andreas Blum; Jark Böttcher; Andreas Heine; Gerhard Klebe; Wibke E Diederich
Structure-guided design of C2-symmetric HIV-1 protease inhibitors based on a pyrrolidine scaffold.
Journal of medicinal chemistry 2008;51(7):2078-87.
2008: Alexander Hillebrecht; Gerhard Klebe
Use of 3D QSAR models for database screening: a feasibility study.
Journal of chemical information and modeling 2008;48(2):384-96.
2007: Naomi Tidten; Bernhard Stengl; Andreas Heine; George A Garcia; Gerhard Klebe; Klaus Reuter
Glutamate versus glutamine exchange swaps substrate selectivity in tRNA-guanine transglycosylase: insight into the regulation of substrate selectivity by kinetic and crystallographic studies.
Journal of molecular biology 2007;374(3):764-76.
2007: Holger Steuber; Paul Czodrowski; Christoph A Sotriffer; Gerhard Klebe
Tracing changes in protonation: a prerequisite to factorize thermodynamic data of inhibitor binding to aldose reductase.
Journal of molecular biology 2007;373(5):1305-20.
2007: Daniel Kuhn; Nils Weskamp; Eyke Hüllermeier; Gerhard Klebe
Functional classification of protein kinase binding sites using Cavbase.
ChemMedChem 2007;2(10):1432-47.
2007: Regina Ortmann; Jochen Wiesner; Katrin Silber; Gerhard Klebe; Hassan Jomaa; Martin Schlitzer
Novel deoxyxylulosephosphate-reductoisomerase inhibitors: fosmidomycin derivatives with spacious acyl residues.
Archiv der Pharmazie 2007;340(9):483-90.
2007: Omid Azim-Zadeh; Alexander Hillebrecht; Uwe Linne; Mohamed A Marahiel; Gerhard Klebe; Klaus Lingelbach; Julius Nyalwidhe
Use of biotin derivatives to probe conformational changes in proteins.
The Journal of biological chemistry 2007;282(30):21609-17.
2007: Bernhard Stengl; Emmanuel A Meyer; Andreas Heine; Ruth Brenk; François Diederich; Gerhard Klebe
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.
Journal of molecular biology 2007;370(3):492-511.
2007: Paul Czodrowski; Christoph A Sotriffer; Gerhard Klebe
Atypical protonation states in the active site of HIV-1 protease: a computational study.
Journal of chemical information and modeling 2007;47(4):1590-8.
2007: Todd J Dolinsky; Paul Czodrowski; Hui Li; Jens Nielsen; Jan H Jensen; Gerhard Klebe; Nathan A Baker
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations.
Nucleic acids research 2007;35(Web Server issue):W522-5.
2007: Peter Block; Nils Weskamp; Alexander Wolf; Gerhard Klebe
Strategies to search and design stabilizers of protein-protein interactions: a feasibility study.
Proteins 2007;68(1):170-86.
2007: Holger Steuber; Matthias Zentgraf; Concettina La Motta; Stefania Sartini; Andreas Heine; Gerhard Klebe
Evidence for a novel binding site conformer of aldose reductase in ligand-bound state.
Journal of molecular biology 2007;369(1):186-97.
2007: Holger Steuber; Andreas Heine; Gerhard Klebe
Structural and thermodynamic study on aldose reductase: nitro-substituted inhibitors with strong enthalpic binding contribution.
Journal of molecular biology 2007;368(3):618-38.
2007: Paul Czodrowski; Christoph A Sotriffer; Gerhard Klebe
Protonation changes upon ligand binding to trypsin and thrombin: structural interpretation based on pK(a) calculations and ITC experiments.
Journal of molecular biology 2007;367(5):1347-56.
2007: Nils Weskamp; Eyke Hüllermeier; Daniel Kuhn; Gerhard Klebe
Multiple graph alignment for the structural analysis of protein active sites.
IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM 2007;4(2):310-20.
2007: Armida Di Fenza; Andreas Heine; Ulrich Koert; Gerhard Klebe
Understanding binding selectivity toward trypsin and factor Xa: the role of aromatic interactions.
ChemMedChem 2007;2(3):297-308.
2007: Christof Gerlach; Martin Münzel; Bernhard Baum; Hans-Dieter Gerber; Tobias Craan; Wibke E Diederich; Gerhard Klebe
KNOBLE: a knowledge-based approach for the design and synthesis of readily accessible small-molecule chemical probes to test protein binding.
Angewandte Chemie (International ed. in English) 2007;46(47):9105-9.
2007: Simone R Hörtner; Tina Ritschel; Bernhard Stengl; Christian Kramer; W Bernd Schweizer; Björn Wagner; Manfred Kansy; Gerhard Klebe; François Diederich
Potent inhibitors of tRNA-guanine transglycosylase, an enzyme linked to the pathogenicity of the Shigella bacterium: charge-assisted hydrogen bonding.
Angewandte Chemie (International ed. in English) 2007;46(43):8266-9.
2007: Christof Gerlach; Michael Smolinski; Holger Steuber; Christoph A Sotriffer; Andreas Heine; David G Hangauer; Gerhard Klebe
Thermodynamic inhibition profile of a cyclopentyl and a cyclohexyl derivative towards thrombin: the same but for different reasons.
Angewandte Chemie (International ed. in English) 2007;46(44):8511-4.
2007: Karen Köhler; Alexander Hillebrecht; Johannes Schulze Wischeler; Alessio Innocenti; Andreas Heine; Claudiu T Supuran; Gerhard Klebe
Saccharin inhibits carbonic anhydrases: possible explanation for its unpleasant metallic aftertaste.
Angewandte Chemie (International ed. in English) 2007;46(40):7697-9.
2007: Matthias Zentgraf; Holger Steuber; Cornelia Koch; Concettina La Motta; Stefania Sartini; Christoph A Sotriffer; Gerhard Klebe
How reliable are current docking approaches for structure-based drug design? Lessons from aldose reductase.
Angewandte Chemie (International ed. in English) 2007;46(19):3575-8.
2006: Clemens Grimm; Ralf Ficner; Tanja Sgraja; Peter Haebel; Gerhard Klebe; Klaus Reuter
Crystal structure of Bacillus subtilis S-adenosylmethionine:tRNA ribosyltransferase-isomerase.
Biochemical and biophysical research communications 2006;351(3):695-701.
2006: Peter Block; Juri Paern; Eyke Hüllermeier; Paul Sanschagrin; Christoph A Sotriffer; Gerhard Klebe
Physicochemical descriptors to discriminate protein-protein interactions in permanent and transient complexes selected by means of machine learning algorithms.
Proteins 2006;65(3):607-22.
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.
Journal of chemical information and modeling 2006;46(6):2737-60.
2006: Paul Czodrowski; Ingo Dramburg; Christoph A Sotriffer; Gerhard Klebe
Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes.
Proteins 2006;65(2):424-37.
2006: Holger Steuber; Matthias Zentgraf; Christof Gerlach; Christoph A Sotriffer; Andreas Heine; Gerhard Klebe
Expect the unexpected or caveat for drug designers: multiple structure determinations using aldose reductase crystals treated under varying soaking and co-crystallisation conditions.
Journal of molecular biology 2006;363(1):174-87.
2006: Alexander Hillebrecht; Claudiu T Supuran; Gerhard Klebe
Integrated approach using protein and ligand information to analyze selectivity- and affinity-determining features of carbonic anhydrase isozymes.
ChemMedChem 2006;1(8):839-53.
2006: Gerhard Klebe
Virtual ligand screening: strategies, perspectives and limitations.
Drug discovery today 2006;11(13-14):580-94.
2006: Samer I Al-Gharabli; Syed T Ali Shah; Steffen Weik; Marco F Schmidt; Jeroen R Mesters; Daniel Kuhn; Gerhard Klebe; Rolf Hilgenfeld; Jörg Rademann
An efficient method for the synthesis of peptide aldehyde libraries employed in the discovery of reversible SARS coronavirus main protease (SARS-CoV Mpro) inhibitors.
Chembiochem : a European journal of chemical biology 2006;7(7):1048-55.
2006: Daniel Kuhn; Nils Weskamp; Stefan Schmitt; Eyke Hüllermeier; Gerhard Klebe
From the similarity analysis of protein cavities to the functional classification of protein families using cavbase.
Journal of molecular biology 2006;359(4):1023-44.
2006: Steffen Weik; Torsten Luksch; Andreas Evers; Jark Böttcher; Christoph A Sotriffer; Andrej Hasilik; Hans-Gerhard Löffler; Gerhard Klebe; Jörg Rademann
The potential of P1 site alterations in peptidomimetic protease inhibitors as suggested by virtual screening and explored by the use of C-C-coupling reagents.
ChemMedChem 2006;1(4):445-57.
2006: Christian Peifer; Thomas Stoiber; Eberhard Unger; Frank Totzke; Christoph Schächtele; Dieter Marmé; Ruth Brenk; Gerhard Klebe; Dieter Schollmeyer; Gerd Dannhardt
Design, synthesis, and biological evaluation of 3,4-diarylmaleimides as angiogenesis inhibitors.
Journal of medicinal chemistry 2006;49(4):1271-81.
2006: Holger Steuber; Matthias Zentgraf; alberto podjarny; Andreas Heine; Gerhard Klebe
High-resolution crystal structure of aldose reductase complexed with the novel sulfonyl-pyridazinone inhibitor exhibiting an alternative active site anchoring group.
Journal of molecular biology 2006;356(1):45-56.
2006: Jasmine Fokkens; Gerhard Klebe
A simple protocol to estimate differences in protein binding affinity for enantiomers without prior resolution of racemates.
Angewandte Chemie (International ed. in English) 2006;45(6):985-9.
2006: Edgar Specker; Jark Böttcher; Sascha Brass; Andreas Heine; Hauke Lilie; Andreas Schoop; Gerhard Müller; Nils Griebenow; Gerhard Klebe
Unexpected novel binding mode of pyrrolidine-based aspartyl protease inhibitors: design, synthesis and crystal structure in complex with HIV protease.
ChemMedChem 2006;1(1):106-17.
2006: 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 research 2006;34(Database issue):D522-6.
2005: Mónica I Esteva; Katja Kettler; Cristina Maidana; Laura Edith Fichera; Andrés M Ruiz; Esteban J Bontempi; Björn Andersson; Hans-Martin Dahse; Peter Haebel; Regina Ortmann; Gerhard Klebe; Martin Schlitzer
Benzophenone-based farnesyltransferase inhibitors with high activity against Trypanosoma cruzi.
Journal of medicinal chemistry 2005;48(23):7186-91.
2005: Bernhard Stengl; Klaus Reuter; Gerhard Klebe
Mechanism and substrate specificity of tRNA-guanine transglycosylases (TGTs): tRNA-modifying enzymes from the three different kingdoms of life share a common catalytic mechanism.
Chembiochem : a European journal of chemical biology 2005;6(11):1926-39.
2005: O Koch; M Bocola; Gerhard Klebe
Cooperative effects in hydrogen-bonding of protein secondary structure elements: a systematic analysis of crystal data using Secbase.
Proteins 2005;61(2):310-7.
2005: Edgar Specker; Jark Böttcher; Andreas Heine; Christoph A Sotriffer; Hauke Lilie; Andreas Schoop; Gerhard Müller; Nils Griebenow; Gerhard Klebe
Hydroxyethylene sulfones as a new scaffold to address aspartic proteases: design, synthesis, and structural characterization.
Journal of medicinal chemistry 2005;48(21):6607-19.
2005: Hans F G Velec; Holger Gohlke; Gerhard Klebe
DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction.
Journal of medicinal chemistry 2005;48(20):6296-303.
2005: Tatiana Petrova; Holger Steuber; Isabelle Hazemann; Alexandra Cousido-Siah; Andre Mitschler; Roland Chung; Mitsuru Oka; Gerhard Klebe; Ossama El-Kabbani; Andrzej Joachimiak; alberto podjarny
Factorizing selectivity determinants of inhibitor binding toward aldose and aldehyde reductases: structural and thermodynamic properties of the aldose reductase mutant Leu300Pro-fidarestat complex.
Journal of medicinal chemistry 2005;48(18):5659-65.
2005: Christof Werner; Milton T Stubbs; R Luise Krauth-Siegel; Gerhard Klebe
The crystal structure of Plasmodium falciparum glutamate dehydrogenase, a putative target for novel antimalarial drugs.
Journal of molecular biology 2005;349(3):597-607.
2005: Katrin Silber; Philipp Heidler; Thomas Kurz; Gerhard Klebe
AFMoC enhances predictivity of 3D QSAR: a case study with DOXP-reductoisomerase.
Journal of medicinal chemistry 2005;48(10):3547-63.
2005: Edgar Specker; Jark Böttcher; Hauke Lilie; Andreas Heine; Andreas Schoop; Gerhard Müller; Nils Griebenow; Gerhard Klebe
An old target revisited: two new privileged skeletons and an unexpected binding mode for HIV-protease inhibitors.
Angewandte Chemie (International ed. in English) 2005;44(20):3140-4.
2005: Katja Kettler; Jochen Wiesner; Katrin Silber; Peter Haebel; Regina Ortmann; Isabel Sattler; Hans-Martin Dahse; Hassan Jomaa; Gerhard Klebe; Martin Schlitzer
Non-thiol farnesyltransferase inhibitors: N-(4-aminoacylamino-3-benzoylphenyl)-3-[5-(4-nitrophenyl)-2 furyl]acrylic acid amides and their antimalarial activity.
European journal of medicinal chemistry 2005;40(1):93-101.
2004: Katrin Kupas; Alfred Ultsch; Gerhard Klebe
Comparison of substructural epitopes in enzyme active sites using self-organizing maps.
Journal of computer-aided molecular design 2004;18(11):697-708.
2004: Andreas Evers; Gerhard Klebe
Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model.
Journal of medicinal chemistry 2004;47(22):5381-92.
2004: Tanja Sgraja; Julia K Ulschmid; Katja Becker; Stephan Schneuwly; Gerhard Klebe; Klaus Reuter; Andreas Heine
Structural insights into the neuroprotective-acting carbonyl reductase Sniffer of Drosophila melanogaster.
Journal of molecular biology 2004;342(5):1613-24.
2004: Andreas Mitsch; Pia Wissner; Markus Böhm; Katrin Silber; Gerhard Klebe; Isabel Sattler; Martin Schlitzer
Non-thiol farnesyltransferase inhibitors: utilization of the far aryl binding site by 5-cinnamoylaminobenzophenones.
Archiv der Pharmazie 2004;337(9):493-501.
2004: Andreas Mitsch; Pia Wissner; Katrin Silber; Peter Haebel; Isabel Sattler; Gerhard Klebe; Martin Schlitzer
Non-thiol farnesyltransferase inhibitors: N-(4-tolylacetylamino-3-benzoylphenyl)-3-arylfurylacrylic acid amides.
Bioorganic & medicinal chemistry 2004;12(17):4585-600.
2004: Nils Weskamp; Daniel Kuhn; Eyke Hüllermeier; Gerhard Klebe
Efficient similarity search in protein structure databases by k-clique hashing.
Bioinformatics (Oxford, England) 2004;20(10):1522-6.
2004: Christoph A Sotriffer; Oliver Krämer; Gerhard Klebe
Probing flexibility and "induced-fit" phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations.
Proteins 2004;56(1):52-66.
2004: Oliver Kraemer; Isabelle Hazemann; alberto podjarny; Gerhard Klebe
Virtual screening for inhibitors of human aldose reductase.
Proteins 2004;55(4):814-23.
2004: Ruth Brenk; Emmanuel A Meyer; Klaus Reuter; Milton T Stubbs; George A Garcia; François Diederich; Gerhard Klebe
Crystallographic study of inhibitors of tRNA-guanine transglycosylase suggests a new structure-based pharmacophore for virtual screening.
Journal of molecular biology 2004;338(1):55-75.
2004: Gerhard Klebe; O Krämer; Christoph A Sotriffer
Strategies for the design of inhibitors of aldose reductase, an enzyme showing pronounced induced-fit adaptations.
Cellular and molecular life sciences : CMLS 2004;61(7-8):783-93.
2004: Daniel Rauh; Gerhard Klebe; Milton T Stubbs
Understanding protein-ligand interactions: the price of protein flexibility.
Journal of molecular biology 2004;335(5):1325-41.
2004: Alexander Weber; Angela Casini; Andreas Heine; Daniel Kuhn; Claudiu T Supuran; Andrea Scozzafava; Gerhard Klebe
Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: new pharmacological opportunities due to related binding site recognition.
Journal of medicinal chemistry 2004;47(3):550-7.
2004: Jochen Wiesner; Katja Kettler; Jacek Sakowski; Regina Ortmann; Alejandro M Katzin; Emilia A Kimura; Katrin Silber; Gerhard Klebe; Hassan Jomaa; Martin Schlitzer
Farnesyltransferase inhibitors inhibit the growth of malaria parasites in vitro and in vivo.
Angewandte Chemie (International ed. in English) 2004;43(2):251-4.
2003: Andreas Evers; Holger Gohlke; Gerhard Klebe
Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials.
Journal of molecular biology 2003;334(2):327-45.
2003: Jeffrey D Kittendorf; Tanja Sgraja; Klaus Reuter; Gerhard Klebe; George A Garcia
An essential role for aspartate 264 in catalysis by tRNA-guanine transglycosylase from Escherichia coli.
The Journal of biological chemistry 2003;278(43):42369-76.
2003: Ruth Brenk; Milton T Stubbs; Andreas Heine; Klaus Reuter; Gerhard Klebe
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.
Chembiochem : a European journal of chemical biology 2003;4(10):1066-77.
2003: Daniel Rauh; Gerhard Klebe; Jörg Stürzebecher; Milton T Stubbs
ZZ made EZ: influence of inhibitor configuration on enzyme selectivity.
Journal of molecular biology 2003;330(4):761-70.
2003: Clemens Grimm; Andreas Evers; Matthias Brock; Claudia Maerker; Gerhard Klebe; Wolfgang Buckel; Klaus Reuter
Crystal structure of 2-methylisocitrate lyase (PrpB) from Escherichia coli and modelling of its ligand bound active centre.
Journal of molecular biology 2003;328(3):609-21.
2003: M Bocola; Milton T Stubbs; Christoph A Sotriffer; B Hauer; T Friedrich; K Dittrich; Gerhard Klebe
Structural and energetic determinants for enantiopreferences in kinetic resolution of lipases.
Protein engineering 2003;16(5):319-22.
2003: Katja Kettler; Jacek Sakowski; Katrin Silber; Isabel Sattler; Gerhard Klebe; Martin Schlitzer
Non-thiol farnesyltransferase inhibitors: N-(4-acylamino-3-benzoylphenyl)-3-[5-(4-nitrophenyl)-2-furyl]acrylic acid amides.
Bioorganic & medicinal chemistry 2003;11(7):1521-30.
2003: Ruth Brenk; Lars Naerum; Ulrich Grädler; Hans-Dieter Gerber; George A Garcia; Klaus Reuter; Milton T Stubbs; Gerhard Klebe
Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis.
Journal of medicinal chemistry 2003;46(7):1133-43.
2003: Judith Günther; Andreas Bergner; Manfred Hendlich; Gerhard Klebe
Utilising structural knowledge in drug design strategies: applications using Relibase.
Journal of molecular biology 2003;326(2):621-36.
2003: Manfred Hendlich; Andreas Bergner; Judith Günther; Gerhard Klebe
Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions.
Journal of molecular biology 2003;326(2):607-20.
2003: Sabine Reyda; Christian Sohn; Gerhard Klebe; Kathrin Rall; Dirk Ullmann; Hans Dieter Jakubke; Milton T Stubbs
Reconstructing the binding site of factor Xa in trypsin reveals ligand-induced structural plasticity.
Journal of molecular biology 2003;325(5):963-77.
2002: Holger Gohlke; Gerhard Klebe
DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein.
Journal of medicinal chemistry 2002;45(19):4153-70.
2002: Sven Grüneberg; Milton T Stubbs; Gerhard Klebe
Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation.
Journal of medicinal chemistry 2002;45(17):3588-602.
2002: Holger Gohlke; Gerhard Klebe
Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors.
Angewandte Chemie (International ed. in English) 2002;41(15):2644-76.
2002: Tobias Jung; Walter Kamm; Armin Breitenbach; Gerhard Klebe; Thomas Kissel
Loading of tetanus toxoid to biodegradable nanoparticles from branched poly(sulfobutyl-polyvinyl alcohol)-g-(lactide-co-glycolide) nanoparticles by protein adsorption: a mechanistic study.
Pharmaceutical research 2002;19(8):1105-13.
2002: Daniel Rauh; Sabine Reyda; Gerhard Klebe; Milton T Stubbs
Trypsin mutants for structure-based drug design: expression, refolding and crystallisation.
Biological chemistry 2002;383(7-8):1309-14.
2002: Christoph A Sotriffer; Holger Gohlke; Gerhard Klebe
Docking into knowledge-based potential fields: a comparative evaluation of DrugScore.
Journal of medicinal chemistry 2002;45(10):1967-70.
2002: Markus Böhm; Gerhard Klebe
Development of new hydrogen-bond descriptors and their application to comparative molecular field analyses.
Journal of medicinal chemistry 2002;45(8):1585-97.
2002: Christoph A Sotriffer; Gerhard Klebe
Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design.
Farmaco (Società chimica italiana : 1989) 2002;57(3):243-51.
2002: Emmanuel A Meyer; Ruth Brenk; Ronald K Castellano; Maya Furler; Gerhard Klebe; François Diederich
De novo design, synthesis, and in vitro evaluation of inhibitors for prokaryotic tRNA-guanine transglycosylase: a dramatic sulfur effect on binding affinity.
Chembiochem : a European journal of chemical biology 2002;3(2-3):250-3.
2002: Milton T Stubbs; Sabine Reyda; Frank Dullweber; Maren Möller; Gerhard Klebe; Dieter Dorsch; Werner W K R Mederski; Hanns Wurziger
pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design.
Chembiochem : a European journal of chemical biology 2002;3(2-3):246-9.
2002: Klaus Reuter; Silke Sanderbrand; Hassan Jomaa; Jochen Wiesner; Irina Steinbrecher; Ewald Beck; Martin Hintz; Gerhard Klebe; Milton T Stubbs
Crystal structure of 1-deoxy-D-xylulose-5-phosphate reductoisomerase, a crucial enzyme in the non-mevalonate pathway of isoprenoid biosynthesis.
The Journal of biological chemistry 2002;277(7):5378-84.
2001: Frank Dullweber; Milton T Stubbs; D Musil; Jörg Stürzebecher; Gerhard Klebe
Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition.
Journal of molecular biology 2001;313(3):593-614.
2001: Walter Kamm; Jörg Hauptmann; Isabel Behrens; Jörg Stürzebecher; Frank Dullweber; H Gohlke; M Stubbs; Gerhard Klebe; Thomas Kissel
Transport of peptidomimetic thrombin inhibitors with a 3-amidino-phenylalanine structure: permeability and efflux mechanism in monolayers of a human intestinal cell line (Caco-2).
Pharmaceutical research 2001;18(8):1110-8.
2001: Dr. Andrea Schafferhans; Gerhard Klebe
Docking ligands onto binding site representations derived from proteins built by homology modelling.
Journal of molecular biology 2001;307(1):407-27.
2001: Ulrich Grädler; Hans-Dieter Gerber; D M Goodenough-Lashua; George A Garcia; Ralf Ficner; Klaus Reuter; Milton T Stubbs; Gerhard Klebe
A new target for shigellosis: rational design and crystallographic studies of inhibitors of tRNA-guanine transglycosylase.
Journal of molecular biology 2001;306(3):455-67.
2000: Clemens Grimm; Edmund Maser; Eric Möbus; Gerhard Klebe; Klaus Reuter; Ralf Ficner
The crystal structure of 3alpha -hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni shows a novel oligomerization pattern within the short chain dehydrogenase/reductase family.
The Journal of biological chemistry 2000;275(52):41333-9.
2000: M L Verdonk; Gerhard Klebe
Simple knowledge-based descriptors to predict protein-ligand interactions. methodology and validation.
Journal of computer-aided molecular design 2000;14(8):787-803.
2000: Clemens Grimm; Gerhard Klebe; Ralf Ficner; Klaus Reuter
Screening orthologs as an important variable in crystallization: preliminary X-ray diffraction studies of the tRNA-modifying enzyme S-adenosyl-methionine:tRNA ribosyl transferase/isomerase.
Acta crystallographica. Section D, Biological crystallography 2000;56(Pt 4):484-8.
2000: Holger Gohlke; Manfred Hendlich; Gerhard Klebe
Knowledge-based scoring function to predict protein-ligand interactions.
Journal of molecular biology 2000;295(2):337-56.
2000: Gerhard Klebe
Recent developments in structure-based drug design.
Journal of molecular medicine (Berlin, Germany) 2000;78(5):269-81.
1999: Ulrich Grädler; Ralf Ficner; George A Garcia; Milton T Stubbs; Gerhard Klebe; Klaus Reuter
Mutagenesis and crystallographic studies of Zymomonas mobilis tRNA-guanine transglycosylase to elucidate the role of serine 103 for enzymatic activity.
FEBS letters 1999;454(1-2):142-6.
1999: Markus Böhm; J St rzebecher; Gerhard Klebe
Three-dimensional quantitative structure-activity relationship analyses using comparative molecular field analysis and comparative molecular similarity indices analysis to elucidate selectivity differences of inhibitors binding to trypsin, thrombin, and factor Xa.
Journal of medicinal chemistry 1999;42(3):458-77.
1999: Gerhard Klebe; T Mietzner; F Weber
Methodological developments and strategies for a fast flexible superposition of drug-size molecules.
Journal of computer-aided molecular design 1999;13(1):35-49.
1999: Gerhard Klebe; U Abraham
Comparative molecular similarity index analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries.
Journal of computer-aided molecular design 1999;13(1):1-10.
1994: Gerhard Klebe; T Mietzner; F Weber
Different approaches toward an automatic structural alignment of drug molecules: applications to sterol mimics, thrombin and thermolysin inhibitors.
Journal of computer-aided molecular design 1994;8(6):751-78.
1994: Gerhard Klebe; U Abraham; T Mietzner
Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity.
Journal of medicinal chemistry 1994;37(24):4130-46.
1994: Gerhard Klebe; T Mietzner
A fast and efficient method to generate biologically relevant conformations.
Journal of computer-aided molecular design 1994;8(5):583-606.
1993: Gerhard Klebe; U Abraham
On the prediction of binding properties of drug molecules by comparative molecular field analysis.
Journal of medicinal chemistry 1993;36(1):70-80.