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Top of the Page
2020
Hassaan, E.; Eriksson, P.-O.; Geschwindner, S.; Heine, A.; Klebe, G.
Comparative Analysis of Fragment Binding to a tRNA-modifying Enzyme using SPR, NMR, and X-ray Crystallography
ChemMedChem
15
, 324-337
Hüfner-Wulsdorf, T.; Klebe, G.
Protein-Ligand Complex Solvation Thermodynamics: Development, Parameterization and Testing of GIST-based Solvent Functionals
J. Chem. Inf. Model.
,
Hüfner-Wulsdorf, T.; Klebe, G.
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.
,
Opassi, G.; Nordström, H.; Lundin, A.; Napolitano, V.; Magari, F.; Dzus, T.; Klebe, G.; Danielson, U. H.
Establishing Trypanosoma cruzi farnesyl pyrophosphate synthase as a viable target for biosensor driven fragment-based lead discovery
Prot. Sci.
, 1-13
Glöckner, S.; Ngo, K.; Sager, C. P.; Hüfner-Wulsdorf, T.; Heine, A.; Klebe, G.
Conformational changes in alkyl chains determine the thermodynamic and kinetic binding profiles of Carbonic Anhydrase Inhibitors
ACS Chem. Biol.
,
Ngo, K.; Collins-Kautz, C.; Gerstenecker, S.; Wagner, B.; Heine, A.; Klebe, G.
Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?
J. Med. Chem.
,
Top of the Page
2019
Badran, M. J.; Bertoletti, N.; Keils, A.; Heine, A.: Klebe, G.; Marchais-Oberwinkler, S.
Mutation and Structural Studies Uncover Crucial Amino Acids Affecting Activity and Stability of 17?-HSD14 Mutational and structural studies uncover crucial amino acids determining activity and stability of 17beta-HSD14
J. Steroid Biochem. Mol. Biol.
189
, 135-144
Wienen-Schmidt, B.; Schmidt, D.; Gerber, H.-D; Heine, A.; Gohlke, H.; Klebe, G.
Surprising Non-Additivity of Methyl-Groups in Drug-Kinase Interaction
ACS Chem. Biol.
14
, 2585-2594
Sandner, A.; Hüfner-Wulsdorf, T.; Heine, A.; Steinmetzer, T.; Klebe, G.
Strategies for Late-stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding
J. Med. Chem.
62
, 9753-9771
Müller, J.; Kirschner, R. A.; Berndt, J.-P.; Wulsdorf, T. ; Metz, A.; Hrdina, R.; Schreiner, P. R.; Geyer, A.; Klebe, G.
Diamondoid Amino Acid-based Peptide Kinase A Inhibitor Analogues
ChemMedChem
14
, 663-672
Klebe, G.
Broad-scale analysis of thermodynamic signatures in medicinal chemistry: are enthalpy-favored binders the better development option?
Drug Discov. Today
24
, 943-948
(review)
Top of the Page
2018
Wienen-Schmidt, B.; Jonker, H. R. A.; Wulsdorf, T.; Gerber, H.-D.; Saxena, K.; Kudlinzki, D.; Sreeramulu, S.; Parigi, G.; Luchinat, C.; Heine, A.; Schwalbe, H.; Klebe G.
Paradoxically, Most Flexible Ligand Binds Most Entropy-Favored: Intriguing Impact of Ligand Flexibility and Solvation on Drug-Kinase Binding
J. Med. Chem.
61
(14)
, 5922-5933
Movsisyan, L. D.; Schäfer, E.; Nguyen, A.; Ehrmann, F. R.; Schwab, A.; Rossolini, T.; Zimmerli, D.; Wagner, B.; Daff, H.; Heine, A.; Klebe, G.; Diederich, F.
Sugar Acetonides are a Superior Motif for Addressing the Large, Solvent-Exposed Ribose-33 Pocket of tRNA-Guanine Transglycosylase
Chem. Eur. J.
24
, 9957-9967
Braun, F.; Bertoletti, N.; Möller, G.; Adamski, J.; Frotscher, M.; Guragossian, N.; Madeira Gírio, P. A.; Le Borgne, M.; Ettouati, L.; Falsong, P.; Müller, S.; Vollmer, G.; Heine, A.; Klebe, G.; Marchais-Oberwinkler, S.
Structure-based design and profiling of novel 17beta-HSD14 inhibitors
Europ. J. Med. Chem.
155
, 61-76
Schiebel, J.; Gaspari, R.; Wulsdorf, T.; Ngo, K.; Sohn, C.; Schrader, T. E.; Cavalli, A.; Ostermann, A; Heine, A.; Klebe, G.
Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes
Nature Comm.
3559
,
Jumde, V. R.; Mondal, M.; Gierse, R.M.; Unver, M. Y.; Magari, F.; van Lier, R. C. W.; Heine, A.; Klebe, G.; Hirsch, A. K. H.
Design and Synthesis of Bioisosteres of Acylhydrazones asStable Inhibitors of the Aspartic Protease Endothiapepsin
ChemMedChem
13
(21)
, 2266-2270
Müller, J.; Kirschner, R. A.; Geyer, A.; Klebe, G.
Conceptional Design of Self-Assembling Bisubstrate-like Inhibitors of Protein Kinase A Resulting in a Boronic Acid Glutamate Linkage
ACS Omega
4
(1)
, 775-784
Wienen-Schmidt, B.; Wulsdorf, T.; Jonker, H. R. A.; Saxena, K.; Kudlinzki, D.; Linhard, V.; Sreeramulu, S.; Heine, A.; Schwalbe, H.; Klebe, G.
On the Implication of Water on Fragment-to-Ligand Growth in Kinase Binding Thermodynamics
ChemMedChem
13
(18)
, 1988-1996
Ehrmann, F. R.; Kalim, J.; Pfaffeneder, T.; Bernet, B.; Hohn, C.; Schäfer, E.; Botzanowski, T.; Cianférani, S.; Heine, A.; Reuter, K.; Diederich, F.; Klebe, G.
Swapping Interface Contacts in the Homodimeric tRNA Guanine Transglycosylase: An Option for Functional Regulation
Angew. Chem. Int Ed. Engl.
57
(32)
, 10085-10090
Top of the Page
2017
Cramer, J.; Schiebel, J.; Wulsdorf, T.; Grohe, K.; Najbauer, E.E.; Ehrmann, F.R.; Radeva, N.; Zitzer, N.; Linne, U.; Linser, R.; Heine, A.; Klebe, G.
A false-positive screening hit in fragment-based lead discovery: watch out for the red herring
Angew. Chem. Int. Ed. Engl.
56
(7)
, 1908-1913
Cramer, J.; Klebe, G.
An allyl protection and improved purification strategy enables the synthesis of functionalized phosphonamidate peptides
SYNTHESIS
49
(8)
, 1857-1866
Cramer, J.; Krimmer, S.G.; Fridh, V.; Wulsdorf, T.; Karlsson, R.; Heine, A.; Klebe, G.
Elucidating the Origin of Long Residence Time Binding for Inhibitors of the Metalloprotease Thermolysin
ACS Chem. Biol.
12
(1)
, 225-233
Ehrmann, F.R.; Stojko, J.; Metz, A.; Debaene, F.; Barandun, L.J.; Heine, A.; Diederich, F.; Cianférani, S.; Reuter, K.; Klebe, G.
Soaking suggests “Alternative Facts”: only Co-Crystallization discloses major ligand-induced interface rearrangements of a homodimeric tRNA-binding protein indicating novel mode-of-inhibition
PLoS One
12
(4)
,
Schiebel, J.; Gaspari, R.; Sandner, A.; Ngo, K.; Gerber, H.D.; Cavalli, A.; Ostermann, A.; Heine, A.; Klebe, G.
Charges shift protonation: neutron diffraction reveals that aniline and 2-aminopyridine become protonated upon binding to trypsin
Angew. Chem. Int. Ed. Engl.
56
(17)
, 4887-4890
Rechlin, C.; Scheer, F.; Terwesten, F.; Wulsdorf, T.; Pol, E.; Fridh, V.; Toth, P.; Diederich W.E.; Heine, A.; Klebe, G.
Price for opening the transient specificity pocket in human aldose reductase upon ligand binding: structural, thermodynamic, kinetic, and computational analysis
ACS Chem. Biol.
12
(5)
, 1397-1415
Dahlke, R.I.; Fraas, S.; Ullrich, K.K.; Heinemann, K.; Romeiks, M.; Rickmeyer, T.; Klebe, G.; Palme, K.; Lüthen, H.; Steffens B
Protoplast swelling and hypocotyl growth depend on different auxin signaling pathways
Plant Physiol
175
(2)
, 982-994
Krimmer, S.G.; Cramer, J.; Schiebel, J.; Heine, A.; Klebe, G.
How Nothing Boosts Affinity: Hydrophobic Ligand Binding to the Virtually Vacated S1? Pocket of Thermolysin
J Am Chem Soc
139
(30)
, 10419-10431
Cramer, J.; Krimmer, S.G.; Heine, A.; Klebe, G.
Paying the Price of Desolvation in Solvent-Exposed Protein Pockets: Impact of Solubilizing Polar Groups on Affinity and Binding Thermodynamics in a Series of Thermolysin Inhibitors
J Med Chem
60
(13)
, 5791-5799
Top of the Page
2016
Rühmann, E.; Rupp, M.; Betz, M.; Heine, A.; Klebe, G.
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
ChemMedChem
11
(3)
, 309-319
Betz, M.; Wulsdorf, T.; Krimmer, S.G.; Klebe, G.
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)
, 223-233
Schiebel, J.; Krimmer, S.G.; Röwer, K.; Knörlein, A.; Wang, X.; Park, A.Y.; Stieler, M.; Ehrmann, F.R.; Fu, K.; Radeva, N.; Krug, M.; Huschmann, F.U.; Glöckner, S.; Weiss, M.S.; Müller, U.; Klebe, G.; Heine A.
High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits
Structure
24
(8)
, 1398-1409
Mondal, M.; Radeva, N.; Fanlo-Virgós, H.; Otto, S.; Klebe, G. Hirsch, A.K.
Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment-Based Drug Design facilitated by Dynamic Combinatorial Chemistry
Angew Chem Int Ed Engl
55
(32)
, 9422-9426
Bertoletti, N.; Braun, F.; Lepage, M.; Möller, G.; Adamski, J.; Heine, A.; Klebe, G.; Marchais-Oberwinkler, S.
New insights into Human 17ß-Hydroxysteroid Dehydrogenase Type 14: first Crystal Structures in Complex with a Steroidal Ligand and with a potent Nonsteroidal Inhibitor
J Med Chem
59
(14)
, 6961-6970
Gaspari, R.; Rechlin, C.; Heine, A.; Bottegoni, G.; Rocchia, W.; Schwarz, D.; Bomke, J.; Gerber, H.D.; Klebe, G.; Cavalli, A.
Kinetic and Structural Insights into the Mechanism of Binding of Sulfonamides to Human Carbonic Anhydrase
J Med Chem
59
(9)
, 4245-4256
Neeb, M.; Hohn, C.; Ehrmann, F.; Härtsch, A.; Heine, A.; Diederich, F.; Klebe, G.
Occupying a flat subpocket in a tRNA-modifying enzyme with ordered or disordered side chains: favorable or unfavorable for binding?
Bioorg Med Chem
24
(20)
, 4900-4910
Radeva, N.; Krimmer, S.; Stieler, M.; Fu, K.; Wang, X.; Ehrmann, F.; Metz, A.; Huschmann, F.; Weiss, M.; Mueller, U.; Schiebel, J.; Heine, A.; Klebe, G.
Experimental active-site mapping by fragments: hot spots remote from the catalytic center of endothiapepsin
J Med Chem
59
(16)
, 7561-7575
Hinkes, S.; Wuttke, A.; Saupe S.M.; Ivanova, T.; Wagner, S.; Knörlein, A.; Heine, A.; Klebe, G.; Steinmetzer, T.
Optimization of cyclic plasmin inhibitors: from benzamidines to benzylamines
J Med Chem
59
(13)
, 6370-6386
Huschmann, F.U.; Linnik, J.; Sparta, K.; Uehlein, M.; Wang, X.; Metz, A.; Schiebel, J.; Heine, A.; Klebe, G.; Weiss, M.S.; Mueller, U.
Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library
Acta Crystallogr F Struct Biol Commun
72
, 346-355
Braun, F.; Bertoletti, N.; Möller, G.; Adamski, J.; Steinmetzer, T.; Salah, M.; van Koppen, C.J.; Heine, A.; Klebe, G.; Marchais-Oberwinkler, S.
First structure-activity relationship of 17?-hydroxysteroid dehydrogenase type 14 nonsteroidal inhibitors and crystal structures in complex with the enzyme
J. Med. Chem.
59
, 10719-10737
Krimmer, S.G.; Cramer, J.; Betz, M.; Fridh; Karlsson, R.; Heine, A.; Klebe, G.
Rational design of thermodynamic and kinetic binding profiles by optimizing surface water networks coating protein-bound ligands
J. Med. Chem.
59
(23)
, 10530-10548
Hohn, C.; Härtsch, A.; Ehrmann, F.R.; Pfaffeneder, T.; Trapp, N.; Dumele, O.; Klebe, G.; Diederich, F.
An Immucillin-based Transition State-Analogous Inhibitor of tRNA–Guanine Transglycosylase (TGT)
Chem. Eur. J.
22
, 6750-6754
Maiwald, A.; Hammami, M.; Wagner, s.; Heine, A.; Klebe, G.; Steinmetzer, T.
Changing the selectivity profile - from substrate analogue thrombin and factor Xa inhibitors to potent matriptase inhibitors
J. Enzym. Inhib.
31
, 89-97
Radeva, N.; Schiebel, J.; Wang, X.; Krimmer, S.G.; Fu, K.; Stieler, M.; Ehrmann, F.R.; Metz, A.; Rickmeyer, T.; Betz, M.; Winquist, J.; Park, A.Y.; Huschmann, F.U.; Weiss, M.S.; Mueller, U; Heine, A.; Klebe, G.
Active Site Mapping of an Aspartic Protease by Multiple Fragment Crystal Structures: Versatile Warheads to Address a Catalytic Dyad
J. Med. Chem.
59
, 9743-9759
Leinweber, M.; Fober, T.; Strickert, M.; Baumgaertner, L.; Klebe, G.; Freisleben, B.; Huellermeier, E.
Large Scale Structural Comparison of Protein Binding Sites Using GPU-based Cloud Computing
IEEE Transactions on knowledge and data engineering
28
, 1423-1434
Schiebel, J.; Radeva, N.; Krimmer, S.G.; Wang, X.; Stieler, M.; Ehrmann, F.R.; Fu, K.; Huschmann F.U.; Metz, A.; Weiss, M.S.; Mueller, U.; Heine, A.; Klebe, G.
Six Biophysical Screening Methods Miss a Large Proportion of Crystallographically Discovered Fragment Hits: A Case Study
ACS Chem. Biol.
11
, 1693-1701
Top of the Page
2015
Stefek, M.; Soltesova, Prnova m.; Majekova, M.; Rechlin, C.; Heine, A.; Klebe, G.
Identification of novel aldose reductase inhibitors based on carboxymethylated mercaptotriazinoindole scaffold
J Med Chem
58
(6)
, 2649-57
Kuhnert, M.; Köster, H.; Bartholomäus, R.; Park, A.Y.; Shahim, A.; Heine, A.; Steuber, H.; Klebe, G.; Diederich, W. E.
Tracing binding modes in hit-to-lead optimization: chameleon-like poses of aspartic protease inhibitors
Angew Chem Int Ed Engl
54
(9)
, 2849-53
Rühmann, E.; Betz, M.; Fricke, M.; Heine, A.; Schäfer, M.; Klebe, G.
Thermodynamic signatures of fragment binding: Validation of direct versus displacement ITC titrations
Biochim Biophys Acta
1850
(4)
, 647-56
Barandun, L.J.; Ehrmann, F.R.; Zimmerli, D.; Immekus, F.; Giroud, M.; Grünenfelder, C.; Schweizer, W.B.; Bernet, B.; Betz, M.; Heine, A.K Klebe, G.; Diederich F.
Replacement of water molecules in a phosphate binding site by furanoside-appended lin-benzoguanine ligands of tRNA-guanine transglycosylase (TGT)
Chem Eur J
1
(21)
, 126-35
Krotzky, T.; Grundwald, C.; Egelerand, U.; Klebe, G.
Large-scale mining for similar protein binding pockets: with RAPMAD retrieval on the fly becomes real
J Chem Inf Model
55
(1)
, 165-79
Klebe, G.
The use of thermodynamic and kinetic data in drug discovery: decisive insight or increasing the puzzlement?
ChemMedChem
10
(2)
, 229-31
Hartmann, A.M.; Mondal, M.; Radeva, N.; Klebe, G.; Hirsch, A.K.
Structure-based optimization of inhibitors of the aspartic protease endothiapepsin
Int J Mol Sci
16
(8)
, 19184-94
Rühmann, E.; Betz, M.; Heine, A.; Klebe, G.
Fragment binding can be either more enthalpy-driven or entropy-driven: crystal structures and residual hydration patterns suggest why
J Med Chem
58
(17)
, 6960-71
Jakobi, S.; Nguyen, P.T.; Debaene, F.; Cianférani, S.; Reuter, K.; Klebe, G.
What Glues a Homodimer Together: Systematic Analysis of the Stabilizing Effect of an Aromatic Hot Spot in the Protein-Protein Interface of the tRNA-modifying Enzyme Tgt
ACS Chem Biol
10
(8)
, 1897-907
Schiebel, J.; Radeva, N.; Köster, H.; Metz, A.; Krotzky, T.; Kuhnert, M.; Diederich, W.E.; Heine, A.; Neumann, L.; Atmanene, C.; Roecklin, D.; Vivat-Hannah, V.; Renaud, J.P.; Meinecke, R.; Schlinck, N.; Sitte, A.; Popp, F.; Zeeb, M.; Klebe, G.
One Question, multiple answers: biochemical and biophysical screening methods retrieve deviating fragment hit leads
ChemMedChem
10
(9)
, 1511-21
Krimmer, S.G.; Klebe, G.
Thermodynamics of protein-ligand interactions as a reference for computational analysis: How to assess accuracy, reliability and relevance of experimental data
Comput Aided Mol Des
29
(9)
, 867-883
Ruiz, F.X.; Cousido-Siah, A.; Porté, S.; Domínguez, M.; Crespo, I.; Rechlin, C.; Mitschler, A.; de Lera, A.R.; Martín, M.J.; de la Fuente, J.A.; Klebe, G.; Parés, X.; Farrés, J.; Podjarny, A.
Structural determinants of the selectivity of 3-benzyluracil-1-acetic acids towards human enzymes Aldose Reductase and AKR1B10
ChemMedChem
10
(12)
, 1989-2003
Krotzky, T.; Klebe, G.
Acceleration of binding site comparisons by graph partitioning
Mol Inform
34
(8)
, 550-558
Klebe, G.
Protein-Ligand Interactions as the Basis for Drug Action, Chapter 7 in © Springer Science+Business Media Dordrecht 2015
G. Scapin et al. (eds.), Multifaceted Roles of Crystallography in Modern Drug Discovery, NATO Science for Peace and Security Series A: Chemistry and Biology
,
(book)
Klebe, G.
Structure-based drug design to perturb function of a tRNA-modifying enzyme by active site and protein-protein interface inhibition, Chapter 16 in © Springer Science+Business Media Dordrecht 2015
Scapin et al. (eds.), Multifaceted Roles of Crystallography in Modern Drug Discovery, NATO Science for Peace and Security Series A: Chemistry and Biology
,
(book)
Klebe, G.
Applying thermodynamic profiling in lead finding and optimization
Nat Rev Drug Discov
14
(2)
, 95-110
(review)
Top of the Page
2014
Grüner, S.; Neeb, M.; Barandun, L.; Sielaff, F.; Hohn, C.; Kojima, S.; Steinmetzer, T.; Diederich, F.; Klebe, G.
Impact of protein and ligand impurities on ITC-derived protein-ligand thermodynamics
Biochim Biophys Acta
1840
(9)
, 2843-2850
Sun, W.; Wendt, M.; Klebe, G.; Röhm, K.H.
On the interpretation of tyrosinase inhibition kinetics
J Enzyme Inhib Med Chem
1
(29)
, 92-99
Mondal, M.; Radeva, N.; Köster, H.; Park, A.; Potamitis, C.; Zervou, M.; Klebe, G.; Hirsch, A.K.
Structure-based design of inhibitors of the aspartic protease endothiapepsin by exploiting dynamic combinatorial chemistry
Angew Chem Int Ed Engl
12
(53)
, 3259-3263
Neeb, M.; Betz, M.; Heine, A.; Barandun, L.J.; Hohn, C.; Diederich, F.; Klebe, G.
Beyond affinity: enthalpy-entropy factorization unravels complexity of a flat structure-activity relationship for inhibition of a tRNA-modifying enzyme
J Med Chem
13
(57)
, 5566-78
Jakobi, S.; Nguyen, T.X.; Debaene, F.; Metz, A.; Sanglier-Cianférani, S.; Reuter, K.; Klebe, G.
Hot-spot analysis to dissect the functional protein-protein interface of a tRNA-modifying enzyme
Proteins
10
(82)
, 2713-32
Neeb, M.; Chzodrowski, P.; Heine, A.; Barandun, L.J.; Hohn, C.; Diederich, F.; Klebe, G.
Chasing protons: how isothermal titration calorimetry, mutagenesis, and pKa calculations trace the locus of charge in ligand binding to a tRNA-binding enzyme
J Med Chem
13
(57)
, 5554-65
Stock, M.; Fober, T.; Hüllermeier, E.; glinca, S.; Klebe, G.; Pahikkala, T.; Airola, A.; De Beaets, B.; Waegeman, W.
Identification of Functionally Related Enzymes by Learning-to-Rank Methods
IEEE/ACM Trans Comput Biol Bioinform
11
(6)
, 1157-1169
Krotzky, T.; Fober, T.; Hüllermeier, E.; Klebe, G.
Extended Graph-Based Models for Enhanced Similarity Search in Cavbase
IEEE/ACM Trans Comput Biol Bioinform
11
(5)
, 878-890
Krotzky, T.; Rickmeyer, T.; Fober, T.; Klebe, G.
Extraction of protein binding pockets in close neighborhood of bound ligands makes comparisons simple due to inherent shape similarity
J Chem Inf Model
54
, 3229-3237
Cousido-Siah, A.; Ruiz, F.X.; Mitschler, A.; Porté, S.; de Lera, A.R.; Martin, M. J.; Manzanaro, S.; de la Fuente, J.A.; Terwesten, F.; Betz, M.; Klebe, G.; Farrés, J.; Parés, X.; Podjarny, A.
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
Biological Crystallography, Acta Crystallographica Section D
70
(3)
, 889-903
Krimmer, S.G.; Betz, M.; Heine, A.; Klebe, G.
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
ChemMedChem
4
(9)
, 833-846
Top of the Page
2013
Samsonova, O.; Glinca, S.; Biela A.; Pfeiffer, C.; Dayyoub, E.; Sahin, D.; Klebe, G.; Kissel, T.
The use of isothermal titration calorimetry and molecular dynamics to show variability in DNA transfection performance
Acta Biomaterialia
9
, 4994-5002
Gersch, M.; Gut, F.; Korotkov, V.S.; Lehmann, J.; Böttcher, T.; Rusch, M.; Hedberg, C.; Waldmann, H.; Klebe, G.; Sieber S.A.
The Mechanism of Caseinolytic Protease (ClpP) Inhibition
Angew Chem Int Ed Engl
52
(10)
, 3009-3014
Schrader, F.C.; Glinca, S.; Sattler, J.M.; Dahse, H.M.; Afanador, G.A.; Prigge, S.T.; Lanzer, M.; Mueller, A.K.; Klebe, G.; Schlitzer, M.
Novel Type II Fatty Acid Biosynthesis (FAS II) Inhibitors as Multistage Antimalarial Agents
ChemMedChem
8
(3)
, 442-461
Saupe, S.M.; Leubner, S.; Betz, M.; Klebe, G.; Steinmetzer, T.
Development of new cyclic plasmin inhibitors with excellent potency and selectivity
J Med Chem
56
(3)
, 820-831
Biela, A.; Nasief, N.N.; Betz, M.; Heine, A.; Hangauer, D.; Klebe, G.
Dissecting the hydrophobic effect on molecular level: the role of water, enthalpy, and entropy in ligand binding to thermolysin
Angew Chem Int Ed Engl
52
(6)
, 1822-1828
Cordes, P.; Sun, W.; Wolber, R.; Kolbe, L.; Klebe, G.; Röhm K. H.
Expression in non-melanogenic systems and purification of soluble variants of human tyrosinase
Biol Chem
394
(5)
, 685-693
Immekus, F.; Barandun, L.J.; Betz, M.; Debaene, F.; Petiot, S.; Sanglier-Cianferani, S.; Reuter, K.; Diederich, F.; Klebe, G.
Launching Spiking Ligands into a Protein-Protein Interface: A Promising Strategy to Destabilize and Break Interface Formation in a tRNA Modifying Enzyme
ACS Chem Biol
8
(6)
, 1163-1178
Biela, I.; Tidten-Luksch, N.; Immekus, F.; Glinca, S.; Nguyen, T.X.; Gerber, H.D.; Heine, A.; Klebe, G.; Reuter, K.
Investigation of Specificity Determinants in Bacterial tRNA-Guanine Transglycosylase Reveals Queuine, the Substrate of Its Eucaryotic Counterpart, as Inhibitor
PLoS One
8
(5)
,
Glinca, S.; Klebe, G.
Cavities tell more than Sequences: Exploring Functional Relationships of Proteases via Binding Pockets
J Chem Inf Model
53
(8)
, 2082-2092
Stieler, M.; Weber, J.; Hils, M.; Kolb, P.; Heine, A.; Büchold, C.; Pasternack, R.; Klebe, G.
Structure of Active Coagulation Factor XIII Triggered by Calcium Binding: Basis for the Design of Next-Generation Anticoagulants
Angew Chem Int Ed Engl
125
(45)
, 12148-12153
Barandun, L. J.; Immekus, F.; Kohler, P.C.; Ritschel, T.; Heine, A.; Orlando, P.; Klebe, G.; Diederich, F.
High-affinity inhibitors of Zymomonas mobilis tRNA-guanine transglycosylase through convergent optimization
Acta Crystallogr D Biol Crystallogr
69
, 1798-1807
Top of the Page
2012
Behnen, J.; Köster, H.; Neudert, G.; Craan, T.; Heine, A.; Klebe, G.
Experimental and Computational Active Site Mapping as a Starting Point to Fragment-based Lead Discovery
ChemMedChem
2
(7)
, 248-261
Toth, P.; Naruhn, S.; Pape, V.; Dörr, S.; Klebe, G.; Müller, R., Diederich, W.
Development of improved PPARß/Delta Inhibitors
ChemMedChem
1
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Biela, A.; Khayat M.; Tan, H.; Kong, J.; Heine, A.; Hangauer, D.; Klebe, G.
Impact of ligand and protein desolvation on ligand binding to the s1 pocket of thrombin
J Mol Biol
418
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Barandun, L. J.; Immekus, F.; Kohler, P. C.; Tonazzi, S.; Wagner, B.; Wendelspiess, S.; Ritschel, T.; Heine, A.; Kansy, M.; Klebe, G.; Diederich, F.
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 Europ. J.
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Biela, A.; Betz, M.; Heine, A.; Klebe, G.
Water makes the Difference: Rearrangement of Water Solvation Layer Triggers Non-additivity of Functional Group Contributions in Protein-Ligand Binding
ChemMedChem
7
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Biela, A.; Sielaff, F.; Terwesten, F.; Heine, A.; Steinmetzer, T.; Klebe, G.
Ligand binding stepwise disrupts water network in thrombin: Enthalpic and entropic changes reveal classical hydrophobic effect
J Med Chem
55
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Reul, R.; Nguyen, J.; Biela, A.; Marxer, E.; Bakowsky, U.; Klebe, G.; Kissel, T.
Biophysical and biological investigation of DNA nano-complexes with a non-toxic, biodegradable amine-modified hyperbranched polyester
Int J Pharm
436
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Gerber, H.D.; Klebe, G.
Concise and efficient syntheses of preQ1 base, Q base, and (ent)-Q base
Org Biomol Chem
436
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Cubrilovic, D.; Biela, A.; Sielaff, F.; Steinmetzer, T.; Klebe, G.; Zenobi, R.
Quantifying protein-ligand binding constants using electrospray ionization mass spectrometry: A systematic binding affinity study of a series of hydrophobically modified trypsin inhibitors
J Am Soc Mass Spectrom
23
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Steinmetzer, T.; Baum, B., Biela, A.; Klebe, G.; Nowak, G.; Bucha, E.
Beyond Heparinization: Design of highly potent thrombin inhibitors suitable for surface coupling
ChemMedChem
7
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Hammami, M.; Rühmann, E.; Maurer, E.; Heine, A.; Gütschow, M.; Klebe, G.; Steinmetzer, T.
New 3-amidinophenylalanine-derived inhibitors of matriptase
MedChemComm
3
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Fober, T.; Mernberger, M.; Klebe, G.; Hüllermeier, E.
Fingerprint Kernels for Protein Structure Comparison
J Mol Inf
31
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Zheng, M.; Pavan, G.M.; Neeb, M.; Schaper, A.K.; Danani, A.; Klebe, G.; Merkel, O.M.; Kissel, T.
Targeting the blind spot of polycationic nanocarrier-based siRNA delivery
ACS Nano
6
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Top of the Page
2011
Brandt, T.; Holzmann, N.; Muley, L.; Khayat, M.; Wegscheid-Gerlach, C.; Baum, B.; Heine, A.; Hangauer, D.; Klebe, G.
Congeneric but Still Distinct: How closely related trypsin ligands exhibit different thermodynamic and structural properties
J Mol Biol
405
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Koch, C.; Heine, A.; Klebe, G.
Tracing the Detail: How Mutations Affect Binding Modes and Thermodynamic Signatures of Closely Related Aldose Reductase Inhibitors
J Mol Biol
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Fober, T.; Glinca, S.; Klebe, G. Hüllermeier, E.
Superposition and alignment of Labeled Point clouds
IEEE/ACM transactions on Computational Biology and Bioinformatics
8
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Schulze Wischeler, J.; Sun, D.; Sandner N. U.; Linne, U.; Heine, A.; Koert, U.; Klebe, G.
Stereo- and Regioselective Azide/Alkyne Cycloadditions in Carbonic Anhydrase II via Tethering, Monitored by Crystallography and Mass Spectrometry
Chemistry Europ. J.
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Spitzmüller, A.; Velec, H. F. G.; Klebe, G.
MiniMuDS: A new Optimizer using Knowledge-Based Potentials improves Scoring of Docking Solutions
J. Chem. Inf. Model.
51
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Blum, A.; Böttcher, J.; Dörr, S.; Heine, A.; Klebe, G.; Diederich, W. E.
Two solutions for the same problem: Multiple binding modes of pyrrolidine-based HIV-1 Protease Inhibitors
J Mol Biol
410
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Mernberger, M.; Klebe, G.; Hüllermeier, E.
SEGA: Semiglobal Graph Alignment for Structure-Based Protein Comparison
IEE/ACM Trans Comput Biol Bioinform
8
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Koch, C.; Heine, A.; Klebe, G.
Radiation damage reveals promising interaction position
J. Synchrotron. Rad.
18
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Koch, C.; Heine, A.; Klebe, G.
Ligand-induced fit affects binding modes and provokes changes in crystal packing of aldose reductase
BBA
1810
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Tomasic, T.; Kovac, A.; Klebe, G.; Blanot, D.; Gobec, S.; Kikelj, D.; Masic, L. P.
Virtual screening for potential inhibitors of bacterial MurC and MurD ligases
J Mol Model
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fconv: Format conversion, manipulation and feature computation of molecular data
Bioinformatics
7
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Fuchs, J. E., Spitzer, G. M.; Javed, A., Biela, A.; Kreutz, C.; Wellenzohn, B.; Liedl, K. R.
Minor groove binders and drugs targeting proteins cover complementary regions in chemical shape space
J Chem Inf Model
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Naruhn, S.; Toth, P. M.; Adhikary, T.; Kaddatz, K.; Pape, V.; Dörr, S.; Klebe, G.; Müller-Brüsselbach, S.; Diederich W. E.; Müller, R.
High-Affinity Peroxisome Proliferator-Activated Receptor β/δ-Specific Ligands with Pure Antagonistic or Inverse Agonistic Properties
Mol Pharmacol
80
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Neudert, G.; Klebe, G.
DSX: A Knowledge-Based Scoring Function for the Assessment of Protein-Ligand Complexes
J Chem Inf Model
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Stegemann, B.; Klebe, G.
Cofactor binding sites in proteins of deviating sequence: Comparative analysis and clustering in torsion angle-, cavity-, and fold-space
Proteins
80
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Schulze Wischer, J.; Heine, A.; Klebe,G.
Introduction of an Artificial Cu Binding Site at the Surface of CA II: Pitfalls of Rational Design Finally Scooped by Serendipity
Current Chemical Biology
5
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Kolb, P.; Klebe, G.
The golden age of GPCR structural biology: any impact on drug design?
Angew Chem Int Ed
50
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Köster, H.; Craan, T.; Brass, S.; Herhaus, C.; Zentgraf, M.; Neumann, L.; Heine, A.; Klebe, G
A Small Nonrule of 3 Compatible Fragment Library Provides High Hit Rate of Endothiapepsin Crystal Structures with Various Fragment Chemotypes
J Med Chem
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Klebe, G.; Schlitzer, M.
M2-Inhibitoren und Neuraminidase-Inhibitoren. Wirkstoffe gegen Grippe
Pharmazie in unserer Zeit
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2010
Janiak, V.; Petersen, M.; Zentgraf, M.; Klebe, G.; Heine, A.
Structure and Substrate Docking of a Hydroxy-(phenyl)pyruvate Reductase
Acta Cryst.
0
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Englert, L.; Silber, K.; Steuber, H.; Brass, S.; Over, B.; Gerber, H.-D.; Heine, A.; Diederich, W. E.; Klebe, G.
Fragment-Based Lead Discovery: Screening and Optimizing Fragments for Thermolysin Inhibition
ChemMedChem
6
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Baum, B.; Muley, L.; Smolinski, M.; Heine, A.; Hangauer, D.; Klebe, G.
Non-additivity of functional group contributions in protein-ligand binding: A Comprehensive Study by Crystallography and Isothermal Titration
J Mol Biol
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Decher, N.; Streit, A. K.; Rapedius, M.; Netter, M. F.; Marzian, S.; Ehling, P.; Schlichthörl, G.; Craan, T.; Renigunta, V.; Köhler, A., Dodel, R. C.; Navarro-Polanco, R. A.; Preisig-Müller, R.; Klebe, G.
RNA Editing modulates the binding of drugs and highly unsaturated fatty acids to the open pore of Kv potassium channels
The EMBO J
29
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Muley, L.; Baum, B.; Smolinski, M.; Freindorf, M.; Heine, A.; Klebe, G, Hangauer, D. G.
Enhancement of Hydrophobic Interactions and Hydrogen Bond Strength by Cooperativity: Synthesis, Modeling and MD-Simulations of a Congeneric Series of Thrombin Inhibitors
J Med Chem
53
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Luksch, T.; Blum, A.; Klee, N.; Diederich, W. E.; Sotriffer, C. A.; Klebe, G.
Pyrrolidine Derivatives as Plasmepsin Inhibitors: Binding Mode Analysis Assisted by Molecular Dynamics Simulations of a Highly Flexible Protein
ChemMedChem
5
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Schulze Wischeler, J.; Innocenti, A.; Vullo, D.; Agrawal, A.; Cohen, S. M.; Heine, A.; Supuran, C. T.; Klebe, G.
Bidentate Zinc Chelators for a-Carbonic Anhydrases that Produce a Trigonal Bipyramidal Coordination Geometry
ChemMedChem
5
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Englert, L.; Biela, A.; Zayed, M.; Heine, A.; Hangauer, A.; Klebe, G.
Displacement of disordered water molecules from hydrophobic pocket creates enthalpic signature: Binding of phosphonamidate to the S(1)'-pocket of thermolysin
Biochim Biophys Acta
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Pfeffer, P.; Fober, T.; Hüllermeier, E.; Klebe, G.
GARLig: A Fully Automated Tool for Subset Selection of Large Fragment Spaces via a Self-Adaptive Genetic Algorithm
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Adding calorimetric data to decision making in lead discovery: a hot tip
Nat Rev Drug Discov.
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2009
Meissner, M.; Koch, O.; Klebe, G.; Schneider, G.
Prediction of turn types in protein structure by machine-learning classifiers.
Proteins
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Koch, O.; Klebe, G.;
Turns revisited: a uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions.
Proteins
74
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Ritschel, T.; Hoertner, S.; Heine, A.; Diederich, F.; Klebe, G.;
Crystal structure analysis and in silico pKa calculations suggest strong pKa shifts of ligands as driving force for high-affinity binding to TGT.
Chembiochem.
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Eisenmann, M.; Steuber, H.; Zentgraf, M.; Altenkämper, M.; Ortmann, R.; Perruchon, J.; Klebe, G.; Schlitzer, M.;
Structure-based optimization of aldose reductase inhibitors originating from virtual screening.
ChemMedChem
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Ramsden, N.L.; Buetow, L.; Dawson, A.; Kemp, L.A.; Ulaganathan, V.; Brenk, R.; Klebe, G.; Hunter, W.N.;
A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphoshate synthase: a target for antimicrobial therapy.
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More than a simple lipophilic contact: a detailed thermodynamic analysis of nonbasic residues in the s1 pocket of thrombin.
J Mol Biol.
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Think twice: understanding the high potency of bis(phenyl)methane inhibitors.
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Fober, T.; Mernberger, M.; Klebe, G.; Hüllermeier, E.;
Evolutionary construction of multiple graph alignments for the structural analysis of biomolecules.
Bioinformatics
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Merging chemical and biological space: Structural mapping of enzyme binding pocket space
Proteins
76
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Kohler, P.C.; Ritschel, T.; Schweizer, W. B.; Klebe, G.; Diederich, F.
High-Affinity inhibitors of tRNA-Guanine Transglycosylase replacing the function of a structural water cluster
Chemistry Europ. J.
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An integrative approach combining noncovalent mass spectrometry, enzyme kinetics and X-ray crystallography to decipher Tgt protein-protein and protein-RNA interaction
J Mol Biol
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Koch, O.; Cole, J.; Block, P.; Klebe, G.
Secbase: Database Module to retrieve secondary structure elements with ligand binding motifs
J Chem Inf Model
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Molecular Docking Screens Using Comparative Models of Proteins
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How to replace the residual solvation shell of polar active site residues to achieve nanomolar inhibition of tRNA-guanine transglycosylase
ChemMedChem
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Wirkstoffdesign : Entwurf und Wirkung von Arzneistoffen.
Spektrum Akademischer Verlag
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Kohring, K.; Wiesner, J.; Altenkämper, M.; Sakowski, J.; Silber, K.; Hillebrecht, A.; Haebel, P.; Dahse, H.M.; Ortmann, R.; Jomaa, H.; Klebe, G.; Schlitzer, M.;
Development of benzophenone-based farnesyltransferase inhibitors as novel antimalarials.
ChemMedChem.
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Perruchon, J.; Ortmann, R.; Altenkämper, M.; Silber, K.; Wiesner, J.; Jomaa, H.; Klebe, G.; Schlitzer, M.;
Studies addressing the importance of charge in the binding of fosmidomycin-like molecules to deoxyxylulosephosphate reductoisomerase.
ChemMedChem.
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Blum, A.; Böttcher, J.; Sammet, B.; Luksch, T.; Heine, A.; Klebe, G.; Diederich, W.E.;
Achiral oligoamines as versatile tool for the development of aspartic protease inhibitors.
Bioorg Med Chem.
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Targeting the open-flap conformation of HIV-1 protease with pyrrolidine-based inhibitors.
ChemMedChem.
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Böttcher, J.; Blum, A.; Heine, A.; Diederich, W.E.; Klebe, G.;
Structural and kinetic analysis of pyrrolidine-based inhibitors of the drug-resistant Ile84Val mutant of HIV-1 protease.
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Structure-guided design of C2-symmetric HIV-1 protease inhibitors based on a pyrrolidine scaffold.
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Computer-aided design and synthesis of nonpeptidic plasmepsin II and IV inhibitors.
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Use of 3D QSAR models for database screening: a feasibility study.
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SFCscore: scoring functions for affinity prediction of protein-ligand complexes.
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Merging the binding sites of aldose and aldehyde reductase for detection of inhibitor selectivity-determining features.
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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.
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DrugScore: profiling protein-ligand interactions using fingerprint simplicity paired with knowledge-based potential fields
ChemCent J
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2007
Hörtner, S.R.; Ritschel, T.; Stengl, B.; Kramer, C.; Schweizer, W.B.; Wagner, B.; Kansy, M.; Klebe, G.; Diederich, F.;
Potent inhibitors of tRNA-guanine transglycosylase, an enzyme linked to the pathogenicity of the Shigella bacterium: charge-assisted hydrogen bonding.
Angew Chem Int Ed Engl.
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Dolinsky, T.J.; Czodrowski, P.; L.i.H.; Nielsen, J.E.; Jensen, J.H.; Klebe, G.; Baker, N.A.;
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations.
Nucleic Acids Res.
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Thermodynamic inhibition profile of a cyclopentyl and a cyclohexyl derivative towards thrombin: the same but for different reasons.
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Atypical protonation states in the active site of HIV-1 protease: a computational study.
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KNOBLE: a knowledge-based approach for the design and synthesis of readily accessible small-molecule chemical probes to test protein binding.
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Use of biotin derivatives to probe conformational changes in proteins.
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Protonation changes upon ligand binding to trypsin and thrombin: structural interpretation based on pK(a) calculations and ITC experiments.
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How reliable are current docking approaches for structure-based drug design? Lessons from aldose reductase.
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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.
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Glutamate versus glutamine exchange swaps substrate selectivity in tRNA-guanine transglycosylase: insight into the regulation of substrate selectivity by kinetic and crystallographic studies.
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Tracing changes in protonation: a prerequisite to factorize thermodynamic data of inhibitor binding to aldose reductase.
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Evidence for a novel binding site conformer of aldose reductase in ligand-bound state.
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Understanding binding selectivity toward trypsin and factor Xa: the role of aromatic interactions.
ChemMedChem.
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Functional classification of protein kinase binding sites using Cavbase.
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Multiple graph alignment for the structural analysis of protein active sites.
IEEE/ACM Trans Comput Biol Bioinform.
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Strategies to search and design stabilizers of protein-protein interactions: a feasibility study.
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Structural and thermodynamic study on aldose reductase: nitro-substituted inhibitors with strong enthalpic binding contribution.
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Supramolecular Structure and Function - Virtual Ligand Screening: A Method to Discover New Drug Leads In “Supramolecular Structure and Function”
Springer
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(book)
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Supramolecular Structure and Function - Novel Leads for Selective Antibiotics against Shigellosis by Virtual Screening, Crystallography and Synthesis
Springer
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2006
Weskamp,N.; ,Klebe,G.;Hüllermeyer,E.;
Wissensentdeckung in strukturbasierten Daten: Graph Alignment zur Analyse von Proteinstrukturen
Magdeburger Wissenschaftsjournal
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Grimm, C.; Ficner, R.; Sgraja, T.; Haebel, P.; Klebe, G.; Reuter, K.;
Crystal structure of Bacillus subtilis S-adenosylmethionine:tRNA ribosyltransferase-isomerase.
Biochem Biophys Res Commun.
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Integrated approach using protein and ligand information to analyze selectivity- and affinity-determining features of carbonic anhydrase isozymes.
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From the similarity analysis of protein cavities to the functional classification of protein families using cavbase.
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Physicochemical descriptors to discriminate protein-protein interactions in permanent and transient complexes selected by means of machine learning algorithms.
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Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein-ligand complexes.
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A simple protocol to estimate differences in protein binding affinity for enantiomers without prior resolution of racemates.
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Steuber, H.; Zentgraf, M.; Gerlach, C.; Sotriffer, C.A.; Heine, A.; Klebe, G.;
Expect the unexpected or caveat for drug designers: multiple structure determinations using aldose reductase crystals treated under varying soaking and co-crystallisation conditions.
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High-resolution crystal structure of aldose reductase complexed with the novel sulfonyl-pyridazinone inhibitor exhibiting an alternative active site anchoring group.
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AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB.
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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.
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An efficient method for the synthesis of peptide aldehyde libraries employed in the discovery of reversible SARS coronavirus main protease (SARS-CoV Mpro) inhibitors.
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Unexpected novel binding mode of pyrrolidine-based aspartyl protease inhibitors: design, synthesis and crystal structure in complex with HIV protease.
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Weber, A.; Böhm, M.; Supuran, C.T.; Scozzafava, A.; Sotriffer, C.A.; Klebe, G.;
3D QSAR selectivity analyses of carbonic anhydrase inhibitors: insights for the design of isozyme selective inhibitors.
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Design, synthesis, and biological evaluation of 3,4-diarylmaleimides as angiogenesis inhibitors.
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Meyer, E. A.; Donati, N.; Guillot, M.; Schweizer, B.; Diederich, F.; Stengl, B.; Brenk, R.; Reuter, K.; Klebe, G.
Synthesis, biological evaluation, and crystallographic studies of extended guanine-based (lin-benzoguanine) inhibitors for tRNA-guanine transglycosylase (TGT)
Helv Chim Acta
89
, 573-597
Brenk,R.; Klebe,G.;
Methods and Principles in Medicinal Chemistry-“Hot Spot” Analysis of Protein-binding Sites as a Prerequisite for Structure-based Virtual Screening and Lead Optimization in Pharmacophores and Pharmacophore Searches
Mannhold, R. / Kubinyi, H. / Folkers
0
,
(book)
Klebe,G.;
Virtual Ligand Screening: Strategies, Perspectives, and Limitations
Drug Discovery Today
11
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(review)
Top of the Page
2005
Petrova, T.; Steuber, H.; Hazemann, I.; Cousido-Siah, A.; Mitschler, A.; Chung, R.; O.k.a.M.; Klebe, G.; El-Kabbani, O.; Joachimiak, A.; Podjarny, A.;
Factorizing selectivity determinants of inhibitor binding toward aldose and aldehyde reductases: structural and thermodynamic properties of the aldose reductase mutant Leu300Pro-fidarestat complex.
J Med Chem.
18
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, 5659-65
Schiffmann, R.; Heine, A.; Klebe, G.; Klein, C.D.;
Metal ions as cofactors for the binding of inhibitors to methionine aminopeptidase: a critical view of the relevance of in vitro metalloenzyme assays.
Angew Chem Int Ed Engl.
23
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Koch, O.; Bocola, M.; Klebe, G.;
Cooperative effects in hydrogen-bonding of protein secondary structure elements: a systematic analysis of crystal data using Secbase.
Proteins.
2
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, 310-7
Velec, H.F.; Gohlke, H.; Klebe, G.;
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.
J Med Chem.
20
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Specker, E.; Böttcher, J.; Heine, A.; Sotriffer, C.A.; Lilie, H.; Schoop, A.; Müller, G.; Griebenow, N.; Klebe, G.;
Hydroxyethylene sulfones as a new scaffold to address aspartic proteases: design, synthesis, and structural characterization.
J Med Chem.
21
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, 6607-19
Specker, E.; Böttcher, J.; Lilie, H.; Heine, A.; Schoop, A.; Müller, G.; Griebenow, N.; Klebe, G.;
An old target revisited: two new privileged skeletons and an unexpected binding mode for HIV-protease inhibitors.
Angew Chem Int Ed Engl.
20
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, 3140-4
Stengl, B.; Reuter, K.; Klebe, G.;
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.
11
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, 1926-39
Silber, K.; Heidler, P.; Kurz, T.; Klebe, G.;
AFMoC enhances predictivity of 3D QSAR: a case study with DOXP-reductoisomerase.
J Med Chem.
10
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, 3547-63
Werner, C.; Stubbs, M.T.; Krauth-Siegel, R.L.; Klebe, G.;
The crystal structure of Plasmodium falciparum glutamate dehydrogenase, a putative target for novel antimalarial drugs.
J Mol Biol.
3
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Top of the Page
2004
Weskamp, N.; Kuhn, D.; Hüllermeier, E.; Klebe, G.;
Efficient similarity search in protein structure databases by k-clique hashing.
Bioinformatics.
10
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Kupas, K.; Ultsch, A.; Klebe, G.;
Comparison of substructural epitopes in enzyme active sites using self-organizing maps.
J Comput Aided Mol Des.
11
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, 697-708
Sgraja, T.; Ulschmid, J.; Becker, K.; Schneuwly, S.; Klebe, G.; Reuter, K.; Heine, A.;
Structural insights into the neuroprotective-acting carbonyl reductase Sniffer of Drosophila melanogaster.
J Mol Biol.
5
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, 1613-24
Ferrara, P.; Gohlke, H.; Price, D.J.; Klebe, G.; Brooks, C.L.3.r.d.;
Assessing scoring functions for protein-ligand interactions.
J Med Chem.
12
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Evers, A.; Klebe, G.;
Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model.
J Med Chem.
22
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, 5381-92
Wiesner, J.; Kettler, K.; Sakowski, J.; Ortmann, R.; Katzin, A.M.; Kimura, E.A.; Silber, K.; Klebe, G.; Jomaa, H.; Schlitzer, M.;
Farnesyltransferase inhibitors inhibit the growth of malaria parasites in vitro and in vivo.
Angew Chem Int Ed Engl.
2
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, 251-4
Evers, A.; Klebe, G.;
Ligand-supported homology modeling of g-protein-coupled receptor sites: models sufficient for successful virtual screening.
Angew Chem Int Ed Engl.
2
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Sotriffer, C.A.; Krämer, O.; Klebe, G.;
Probing flexibility and "induced-fit" phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations.
Proteins.
1
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Brenk, R.; Meyer, E.A.; Reuter, K.; Stubbs, M.T.; Garcia, G.A.; Diederich, F.; Klebe, G.;
Crystallographic study of inhibitors of tRNA-guanine transglycosylase suggests a new structure-based pharmacophore for virtual screening.
J Mol Biol.
1
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Rauh, D.; Klebe, G.; Stubbs, M.T.;
Understanding protein-ligand interactions: the price of protein flexibility.
J Mol Biol.
5
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Kraemer, O.; Hazemann, I.; Podjarny, A.D.; Klebe, G.;
Virtual screening for inhibitors of human aldose reductase.
Proteins.
4
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, 814-23
Weskamp, N.; Hüllermeier, E.; Kuhn, D.; Klebe, G.;
Graph Alignments: A New Concept to Detect Conserved Regions in Protein Active Sites
Robert Giegerich, Jens Stoye (eds.) Proceedings of the German Conference on Bioinformatics 2004
0
, 131-140
Weber, A.; Casini, A.; Heine, A.; Kuhn, D.; Supuran, C. T.; Scozzafava, Klebe, G.
Unexpected Nanomolar Inhibition of Carbonic Anhydrase by COX-2-Selective Celecoxib: New Pharmacological Opportunities due to Related Binding Site Recognition
J. Med. Chem.
47
, 550-557
Meyer, E. A.; Furler, M.; Diederich, F.; Brenk, R.; Klebe, G.
Synthesis and In Vitro Evaluation of 2-aminoquinazolin-4(3H)-one-based Inhibitors for tRNA-Guanine Transglycosylase (TGT)
Helv. Chim. Acta
87
, 1333-1356
Klebe,G.;
In Supramolecular Structure and Function - Differences in Binding of Stereoisomers to Protein Active Sites
Kluwer Academic/Plenum Pub., New York, U.S.A.
0
,
(book)
Klebe,G.;
In Virtual Screening in Drug Discovery- Virtual Screening: Scope and Limitations
CRC Press, Boca Raton, FL, USA
0
,
(book)
Klebe,G.;
Chemoinformatics, Eds. J. Gasteiger and T. Engel- From Structural Genomics to Drug Design: Knowledge Discovery in Crystallographic Databases to Assist Lead Discovery and Optimization
Wiley-VCH
0
,
(book)
Sotriffer, C.A.;Klebe, G.;
Chemoinformatics, Eds. J. Gasteiger and T. Engel, Vol. 4, The Docking Problem
Wiley-VCH
0
,
(book)
Klebe,G.;
Lead Identification in Post-genomics: Computers as a Complementary Alternative
Drug Discov. Today
3
, 225-230
(review)
Klebe,G.;
New Leads out of the Computer
Screening - Trends in Drug Discovery
5
, 18-20
(review)
Klebe,G.;
Neue Leitstrukturen aus dem Computer
Biospektrum
3
, 266-268
(review)
Antel,J.; Weber,A.; Sotriffer, C.A.; Klebe,G.;
Multiple binding modes observed in X-ray structures of carbonic anhydrase-inhibitor complexes and elsewhere: Consequences for Structure-Based Drug Design, in Carbonic Anhydrase: Its Inhibitors and Activators
J. Conway crc Enzyme Inhibitors Sieries, CRC Press
0
, 45-65
(review)
Klebe,G.; Krämer, O. ; Sotriffer,C;
Strategies for the Design of Inhibitors of Aldose Reductase, an Enzyme showing Pronounced Induced-Fit Adaptations
Cell. Mol. Life Sci.
61
, 783-793
(review)
Stubbs, MT; Klebe, G.;
Das Nadelöhr – Von der Forschung zur Entwicklung
Die Pharmazeutische Industrie: Einblick, Durchblick, Perspektive
0
, 35-64
(review)
Diederich,W.; Heine,A.; Haebel,P.; Reuter,K.; Sotriffer,C.;Klebe,G.;
Struktur-basierte Arzneistoffsuche und Synthese: neue Konzepte schneller ans Ziel zu kommen
Laborpraxis
11
, 24-26
(review)
Top of the Page
2003
Evers, A.; Gohlke, H.; Klebe, G.;
Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials.
J Mol Biol.
2
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Boström, J.; Böhm, M.; Gundertofte, K.; Klebe, G.;
A 3D QSAR study on a set of dopamine D4 receptor antagonists.
J Chem Inf Comput Sci.
3
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, 1020-7
Kettler, K.; Sakowski, J.; Silber, K.; Sattler, I.; Klebe, G.; Schlitzer, M.;
Non-thiol farnesyltransferase inhibitors: N-(4-acylamino-3-benzoylphenyl)-3-[5-(4-nitrophenyl)-2-furyl]acrylic acid amides.
Bioorg Med Chem.
7
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, 1521-30
Rauh, D.; Klebe, G.; Stürzebecher, J.; Stubbs, M.T.;
ZZ made EZ: influence of inhibitor configuration on enzyme selectivity.
J Mol Biol.
4
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, 761-70
Grimm, C.; Evers, A.; Brock, M.; Maerker, C.; Klebe, G.; Buckel, W.; Reuter, K.;
Crystal structure of 2-methylisocitrate lyase (PrpB) from Escherichia coli and modelling of its ligand bound active centre.
J Mol Biol.
3
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, 609-21
Kittendorf, J.D.; Sgraja, T.; Reuter, K.; Klebe, G.; Garcia, G.A.;
An essential role for aspartate 264 in catalysis by tRNA-guanine transglycosylase from Escherichia coli.
J Biol Chem.
43
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Brenk, R.; Stubbs, M.T.; Heine, A.; Reuter, K.; Klebe, G.;
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.
10
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, 1066-77
Bocola, M.; Stubbs, M.T.; Sotriffer, C.; Hauer, B.; Friedrich, T.; Dittrich, K.; Klebe, G.;
Structural and energetic determinants for enantiopreferences in kinetic resolution of lipases.
Protein Eng.
5
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, 319-22
Brenk, R.; Naerum, L.; Grädler, U.; Gerber, H.D.; Garcia, G.A.; Reuter, K.; Stubbs, M.T.; Klebe, G.;
Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis.
J Med Chem.
7
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, 1133-43
Günther, J.; Bergner, A.; Hendlich, M.; Klebe, G.;
Utilising structural knowledge in drug design strategies: applications using Relibase.
J Mol Biol.
2
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Hendlich, M.; Bergner, A.; Günther, J.; Klebe, G.;
Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions.
J Mol Biol.
2
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, 607-20
Reyda, S.; Sohn, C.; Klebe, G.; Rall, K.; Ullmann, D.; Jakubke, H.D.; Stubbs, M.T.;
Reconstructing the binding site of factor Xa in trypsin reveals ligand-induced structural plasticity.
J Mol Biol.
5
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, 963-77
Brenk, R.; Gerber, H.D.; Kittendorf, J.; Garcia, G. A.; Reuter, K.; Klebe, G.
From Hit to Lead: De Novo Design based on Virtual Screening Hits of Inhibitors of tRNA-guanine transglycosylase, a putative Target of Shigellosis Therapy
Helv. Chim. Acta
86
, 1435-1452
Klebe,G.;
Neue Leitstrukturen für die Arzneimittelentwicklung aus dem Computer
Bioforum
10
, 614-6
(review)
Sotriffer, C.A.;Klebe, G.; Stahl, M.; Böhm HJ
Burger's Medicinal Chemistry and Drug Discovery, Vol. 1,-Docking and Scoring Functions / Virtual Screening
Wiley,
0
, 281-333
(review)
Top of the Page
2002
Jung, T.; Kamm, W.; Breitenbach, A.; Klebe, G.; Kissel, T.;
Loading of tetanus toxoid to biodegradable nanoparticles from branched poly(sulfobutyl-polyvinyl alcohol)-g-(lactide-co-glycolide) nanoparticles by protein adsorption: a mechanistic study.
Pharm Res.
8
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, 1105-13
Sotriffer, C.A.; Gohlke, H.; Klebe, G.;
Docking into knowledge-based potential field: A comparative evaluation of DrugScore
J. Med. Chem.
45
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Schmitt, S.; Kuhn, D.; Klebe, G.;
A new method to detect related function among proteins independent of sequence and fold homology.
J Mol Biol.
2
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Gohlke, H.; Klebe, G.;
DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein.
J Med Chem.
19
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Grüneberg, S.; Stubbs, M.T.; Klebe, G.;
Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation.
J Med Chem.
17
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Rauh, D.; Reyda, S.; Klebe, G.; Stubbs, M.T.;
Trypsin mutants for structure-based drug design: expression, refolding and crystallisation.
Biol Chem.
7
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, 1309-14
Gohlke, H.; Klebe, G.;
Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors.
Angew Chem Int Ed Engl.
15
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, 2644-76
Reuter, K.; Sanderbrand, S.; Jomaa, H.; Wiesner, J.; Steinbrecher, I.; Beck, E.; Hintz, M.; Klebe, G.; Stubbs, M.T.;
Crystal structure of 1-deoxy-D-xylulose-5-phosphate reductoisomerase, a crucial enzyme in the non-mevalonate pathway of isoprenoid biosynthesis.
J Biol Chem.
7
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, 5378-84
Meyer, E.A.; Brenk, R.; Castellano, R.K.; Furler, M.; Klebe, G.; Diederich, F.;
De novo design, synthesis, and in vitro evaluation of inhibitors for prokaryotic tRNA-guanine transglycosylase: a dramatic sulfur effect on binding affinity.
Chembiochem.
2
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Abbate, F.; Supuran, C.T.; Scozzafava, A.; Orioli, P.; Stubbs, M.T.; Klebe, G.;
Nonaromatic sulfonamide group as an ideal anchor for potent human carbonic anhydrase inhibitors: role of hydrogen-bonding networks in ligand binding and drug design.
J Med Chem.
17
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Böhm, M.; Klebe, G.;
Development of new hydrogen-bond descriptors and their application to comparative molecular field analyses.
J Med Chem.
8
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, 1585-97
Stubbs, M.T.; Reyda, S.; Dullweber, F.; Möller, M.; Klebe, G.; Dorsch, D.; Mederski, W.W.; Wurziger, H.;
pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design.
Chembiochem.
2
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Klebe,G.;
From Genes to Drugs via Crystallography Ed. N. Borkakoti, Erice Crystallogr. Publ. - Structural and Energetic Aspects of Protein-Ligand Binding in Drug Design
0
,
(book)
Klebe,G.;
Small Molecule-Protein Interaction- Schering Foundation in Ernst Schering Research Foundation Workshop 42-From Structure to Recognition Principles: Mining in Crystal Data as a Prerequiste for Drug Design
Springer Verl.
0
,
(book)
Klebe,G.;
Handbook of Experimental Pharmacology, Stereochemical Aspects of Drug Action and Disposition-Binding Differences of Stereoisomers at Protein Binding Sites
Springer Verlag, Heidelberg
0
,
(book)
Klebe,G.;
Innovative lead discovery: From geometry to function and ligand design
Curr. Drug Discovery
7
, 27-30
(review)
Sotriffer, C.A.;Klebe, G.;
Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design
IL Farmaco
57
, 243-251
(review)
Top of the Page
2001
Grüneberg, S.; Wendt, B.; Klebe, G.;
Subnanomolar Inhibitors from Computer Screening: A Model Study Using Human Carbonic Anhydrase II.
Angew Chem Int Ed Engl.
2
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, 389-393
Bergner, A.; Günther, J.; Hendlich, M.; Klebe, G.; Verdonk, M.;
Use of Relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects.
Biopolymers.
2
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, 99-110
Dullweber, F.; Stubbs, M.T.; Musil, D.; Stürzebecher, J.; Klebe, G.;
Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition.
J Mol Biol.
3
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, 593-614
Kamm, W.; Hauptmann, J.; Behrens, I.; Stürzebecher, J.; Dullweber, F.; Gohlke, H.; Stubbs, M.; Klebe, G.; Kissel, T.;
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).
Pharm Res.
8
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Schafferhans, A.; Klebe, G.;
Docking ligands onto binding site representations derived from proteins built by homology modelling.
J Mol Biol.
1
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Gohlke, H.; Klebe, G.;
Statistical potentials and scoring functions applied to protein-ligand binding.
Curr Opin Struct Biol.
2
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Grädler, U.; Gerber, H.D.; Goodenough-Lashua, D.M.; Garcia, G.A.; Ficner, R.; Reuter, K.; Stubbs, M.T.; Klebe, G.;
A new target for shigellosis: rational design and crystallographic studies of inhibitors of tRNA-guanine transglycosylase.
J Mol Biol.
3
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Schmitt, S.; Hendlich, M.; Klebe, G.
From structure to function: A new approach to detect functional similarity among proteins independent from sequence and fold homology
Angew. Chem. Int. Ed.
40
, 3141-3144
Kraemer, O; Böhm, M.;Schlitzer, M.; Klebe, G.;
Rational Approaches to Drug Design- 3D QSAR Analysis in Case of a Flexible Protein: CoMSIA Model for a Series of Aldose Reductase Inhibitors with Various Binding Modes
Prous Sci
0
,
(book)
Gohlke,H.; Dullweber,F.; Kamm,W.; März,J.; Kissel,T.; Klebe, G.;
Rational Approaches to Drug Design-Prediction of Human Intestinal Absorption Using a Combined “Simulated Annealing/Backpropagation Neural Network” Approach
Prous Sci
0
,
(book)
Nissink,JWM; Verdonk,ML; Klebe, G.;
Rational Approaches to Drug Design-Knowledge-based Descriptors to Predict Protein-Ligand Interactions
Prous Sci
0
,
(book)
Schmitt, S.; Hendlich,M.; Klebe, G.;
Rational Approaches to Drug Design-Development of a Database for Protein Cavities and its Usage for Similarity Searches in Binding Sites
Prous Sci
0
,
(book)
Stahl,M.; Rarey, M.;Klebe,G.;
Methods and Principles in Medicinal Chemistry, From Genomics to Drugs”, Ed. T. Lengauer,Vol 14- Screening of Drug Databases
Wiley-VCH, Weinheim
0
,
(book)
Stahl,M.; Rarey, M.;Klebe,G.;
Thermodynamics of Drug-Receptor Interactions,Ed. R. Raffa - Thermodynamic Models of Drug-Receptor Interactions: A General Introduction
John Wiley & Sons, New York
0
,
(book)
Klebe,G.;
Wirkstoffdesign bei der Entwicklung substratähnlicher HIV-Protease-Hemmstoffe
Pharm.u.Zeit
0
, 55-76
(review)
Top of the Page
2000
Escherich, A.; Lutz, J.; Escrieut, C.; Fourmy, D.; Neuren, v.a.n.A.S.; Möller, G.; Schafferhans, A.; Klebe, G.; Moroder, L.;
Peptide/benzodiazepine hybrids as ligands of CCK(A) and CCK(B) receptors.
Biopolymers.
2
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, 55-76
Grimm, C.; Maser, E.; Möbus, E.; Klebe, G.; Reuter, K.; Ficner, R.;
The crystal structure of 3alpha -hydroxysteroid dehydrogenase/carbonyl reductase from Comamonas testosteroni shows a novel oligomerization pattern within the short chain dehydrogenase/reductase family.
J Biol Chem.
52
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Nissink, J.W.M.; Verdonk, M.L.; Klebe, G.;
Simple knowledge-based descriptors to predict protein-ligand interactions. methodology and validation.
J Comput Aided Mol Des.
8
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, 787-803
Grimm, C.; Klebe, G.; Ficner, R.; Reuter, K.;
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 Crystallogr D Biol Crystallogr.
0
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Gohlke, H.; Hendlich, M.; Klebe, G.;
Knowledge-based scoring function to predict protein-ligand interactions.
J Mol Biol.
2
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Calderone, V.; Chevrier, B.; Zandt, V.a.n.M.; Lamour, V.; Howard, E.; Poterszman, A.; Barth, P.; Mitschler, A.; L.u.J.; Dvornik, D.M.; Klebe, G.; Kraemer, O.; Moorman, A.R.; Moras, D.; Podjarny, A.;
The structure of human aldose reductase bound to the inhibitor IDD384.
Acta Crystallogr D Biol Crystallogr.
0
, 536-40
Gohlke, H.; Hendlich, M.; Klebe, G.
Prediction of Binding Modes, Binding Affinities, and "Hot Spots" for Protein-Ligand Complexes Using a Knowledge-based Scoring Function
Persp. Drug Discov. Design
20
(1)
, 115-144
Klebe,G.; Grädler,U.; Grüneberg,S.; Krämer,O.; Gohlke,H.;
Virtual Screening for Bioactive Molecules, Eds. H.J. Böhm, S. Schneider- Understanding Receptor-Ligand Interactions as a Prerequisite for Virtual Screening
Wiley-VCH, Weinheim
0
,
(book)
Klebe,G.;
Virtual Screening: An Alternative or Complement to High Throughput Screening?
Editor, Kluwer Academic Publ.
0
,
(book)
Dullweber,F.; Sevenich,FW;Klebe,G.;
Molecular Modelling and Prediction of Bioactivity-Ed. K. Gundertofte and F. Jorgensen- Determination of Accurate Thermodynamics of Binding for Proteinase-Inhibitor Interactions
KLUWER Academic /Plenum Publ., New York
0
,
(book)
Klebe,G.; Böhm,M.; Dullweber,F.; Grädler,U.; Gohlke,H.; Hendlich,M.;
Molecular Modelling and Prediction of Bioactivity-Ed. K. Gundertofte and F. Jorgensen- Structural and Energetic Aspects of Protein-Ligand Binding in Drug Design
KLUWER Academic /Plenum Publ., New York
0
,
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Klebe,G.;
Recent Developments in Structure-based Drug Design
J. Mol. Med.
0
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Top of the Page
1999
Grädler, U.; Ficner, R.; Garcia, G.A.; Stubbs, M.T.; Klebe, G.; Reuter, K.;
Mutagenesis and crystallographic studies of Zymomonas mobilis tRNA-guanine transglycosylase to elucidate the role of serine 103 for enzymatic activity.
FEBS Lett.
1
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Nielsen, J.E.; Andersen, K.V.; Honig, B.; Hooft, R.W.; Klebe, G.; Vriend, G.; Wade, R.C.;
Improving macromolecular electrostatics calculations.
Protein Eng.
8
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Neuren, v.a.n.A.S.; Müller, G.; Klebe, G.; Moroder, L.;
Molecular modelling studies on G protein-coupled receptors: from sequence to structure?
J Recept Signal Transduct Res.
1
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Böhm, M.; Stürzebecher,J.; Klebe, G.;
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 f
J Med Chem.
3
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Klebe, G.; Mietzner, T.; Weber, F.;
Methodological developments and strategies for a fast flexible superposition of drug-size molecules.
J Comput Aided Mol Des.
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Klebe, G.; Abraham, U.;
Comparative molecular similarity index analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries.
J Comput Aided Mol Des.
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, 1-10
Hoegl,L.; Korting,HC; Klebe,G;
Inhibitors of Aspartic Proteases in Human Diseases: Molecular Modeling Comes of Age
Die Pharmazie
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Top of the Page
1998
Lemmen, C.; Lengauer, T.; Klebe, G.;
FLEXS: a method for fast flexible ligand superposition.
J Med Chem.
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Klebe, G.;
Recent Trends in Molecular Recognition-Eds. F. Diederich, H. Künzer- New Tools for Drug Design Based on Protein Ligand Recognition Principles
Springer Verl. Berlin, Heidelberg, New York
0
,
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Klebe, G.;
Rational Molecular Design in Drug Research, Alfred Benzon Symposium, No. 42-Eds. -Eds. T. Lilijefors, F.S. Jorgensen, P. Krogsgaard-Larsen- Molecular Similarity - A Guideline for the Design of New Protein Ligands
Munksgaard Publ.
0
,
(book)
Klebe, G.;
Crystallographic Database Knowledge: Starting Point for New Computer Tools in Drug Design
Periodicum Biologorum
0
, 85-91
(review)
Klebe, G.;
Comparative Molecular Similarity Indices Analysis - CoMSIA
Persp. Drug Discov. Design
12
, 87-104
(review)
Klebe, G.; Böhm,H.J.;
Energetic and Entropic Factors Determining Binding Affinity in Protein-Ligand Complexes
Periodicum Biologorum
100
, 77-83
(review)
Klebe, G.;
Success Stories in Structure-based Drug Design
Periodicum Biologorum
100
, 93-98
(review)
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1997
Erk,P.; hünig,S.; Klebe,G.;Metzenthin,T.; Werner,HP; v.Schütz,JU.;
2,3-Disubstituted 1,4-Benzoquinones and their N,N-Dicyanimines: Syntheses, Physical Properties, and CT Complexes with TTF
Liebigs Ann./Recuiel
0
, 1235-43
Klebe, G.; Böhm, H.J.;
Energetic and entropic factors determining binding affinity in protein-ligand complexes.
J Recept Signal Transduct Res.
1
(17)
, 459-73
Nissink, J.W.M.; Verdonk, M.L.; Kroon,J.;Klebe, G.; Mietzner,T.;
Superposition of Molecules. Electron Density Fitting by Application of Fourier Transforms
J. Comput. Chem.
18
, 638-645
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1996
Klebe, G.;Hädicke,E.; Böhm KH.; Reuther,W.; Hickmann,E.;
Die Molekül- und Kristallstruktur der Kupfer-, Aluminium- und Kaliumkomplexe des Cyclohexyl-hydroxy-diazeniumoxids.
Z. Krist.
211
, 798-803
Böhm,HJ.; brode,S.; Hesse,U.; Klebe,G.;
Oxygen and Nitrogen in Competitive Situations: Which Is The Hydrogen-Bond Acceptor?
Chem. Eur. J.
2
, 1509-13
Barnickel,G.; Gasteiger,J.; Klebe,G.;Levy,P.; Zell,A.;
Neue Leitstrukturen aus dem Computer
Nachr. Chem. Tech. Lab.
44
, 863-72
Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G.;
A fast flexible docking method using an incremental construction algorithm.
J Mol Biol.
3
(261)
, 470-89
Böhm,HJ.; Klebe,G.; Kubinyi,H.;
Wirkstoffdesign - Der Weg zum Arzneimittel
Spektrum - Akademischer Verlag
0
,
(book)
Böhm,HJ.; Klebe,G.;
What Can We Learn From Molecular Recognition in Protein-Ligand Complexes for the Design of New Drugs?
Angew. Chem. Int. Ed. Engl.
35
, 2588-2614
(review)
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1995
Brana, M.F.; Castellano, J.M.; Moran, M.; Emling, F.; Kluge, M.; Schlick, E.; Klebe, G.; Walker, N.;
Synthesis, structure and antitumor activity of new benz[d,e]isoquinoline-1,3-diones.
Arzneimittelforschung.
12
(45)
, 1311-8
Steiner,G.; Munschauer,R.; Klebe,G.; Siggel,L:;
Diastereoselective Synthesis of Exo-6-aryl-3-aza-bicyclo[3.2.0]heptane Derivatives by intramolecular [2+2]-Photocycloaddition of Diallylic Amines
Heterocycles
40
, 319-330
Klebe, G.;
Toward a More Efficient Handling of Conformational Flexibility in Computer-Assisted Modelling of Drug Molecules
Persp. Drug Discov. and Design
3
, 85-105
(review)
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1994
Klebe, G.; Abraham, U.; Mietzner, T.;
Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity.
J Med Chem.
24
(37)
, 4130-46
Klebe, G.; Mietzner, T.; Weber, F.;
Different approaches toward an automatic structural alignment of drug molecules: applications to sterol mimics, thrombin and thermolysin inhibitors.
J Comput Aided Mol Des.
6
(8)
, 751-78
Sadowski,J.;Gasteiger,J.; Klebe,G.;
Comparison of Automatic Three-Dimensional Model Builders Using 639 X-ray Structures
J. Chem. Inf. Comput. Sci
34
, 1000-8
Klebe, G.; Mietzner, T.;
A fast and efficient method to generate biologically relevant conformations.
J Comput Aided Mol Des.
5
(8)
, 583-606
Klebe, G.;
The use of composite crystal-field environments in molecular recognition and the de novo design of protein ligands.
J Mol Biol.
2
(237)
, 212-35
Klebe, G.;
Mapping Common Molecular Fragments in Crystal Structures to Explore Conformation and Configuration Space under the Conditions of a Molecular Environment
J. Mol. Struct. (Theochem)
308
, 53-89
Klebe, G.;Weber,F.;
Description of Coordination Geometry in Tetrahedral Metal Complexes by Symmetry Deformation Coordinates
Acta Crystallogr. Sect. B.
0
, 50-9
Klebe, G.; Mietzner,T.;
Correlations, Transformations and Interactions in Organic Crystal Chemistry- Ed. D.W. Jones and A. Katrusiak, IUCr Crystallographic Symposia 7-Correlation of Crystal Data to Analyze and Predict Ligand/Receptor Interactions
Oxford Science Publ
0
,
(book)
Klebe, G.;
Structure Correlation- Ed. H.B. Bürgi und J.D. Dunitz-Structure Correlation and Ligand/Receptor Interactions
VCH
0
,
(book)
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1993
Klebe, G.; Diederich,F.;
A Comparison of the Crystal Packing in Benzene with the Geometry Seen in Crystalline Cyclophane-Benzene Complexes: Guidelines for Rational Receptor Design
Phil. Trans. Royal Soc. London A
345
, 37-48
Klebe, G.; Abraham, U.;
On the prediction of binding properties of drug molecules by comparative molecular field analysis.
J Med Chem.
1
(36)
, 70-80
Klebe, G.;
3D-QSAR and Drug Design- Ed. H. Kubinyi - Structural Alignment of Molecules
0
,
(book)
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