Search Results - "KLEBE, Gerhard"

Applying thermodynamic profiling in lead finding and optimization by Klebe, Gerhard

“…Thermodynamic profiling of protein–ligand binding is increasingly used during lead optimization to find ligands that bind with high affinity. In this…”
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Virtual ligand screening: strategies, perspectives and limitations by Klebe, Gerhard

“…In contrast to high-throughput screening, in virtual ligand screening (VS), compounds are selected using computer programs to predict their binding to a target…”
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DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes by Neudert, Gerd, Klebe, Gerhard

“…We introduce the new knowledge-based scoring function DSX that consists of distance-dependent pair potentials, novel torsion angle potentials, and newly…”
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Adding calorimetric data to decision making in lead discovery: a hot tip by Ladbury, John E, Klebe, Gerhard, Freire, Ernesto

“…Isothermal titration calorimetry can be used to obtain thermodynamic data on the binding of compounds to protein targets. Ladbury and colleagues propose that…”
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Intriguing role of water in protein-ligand binding studied by neutron crystallography on trypsin complexes by Schiebel, Johannes, Gaspari, Roberto, Wulsdorf, Tobias, Ngo, Khang, Sohn, Christian, Schrader, Tobias E., Cavalli, Andrea, Ostermann, Andreas, Heine, Andreas, Klebe, Gerhard

“…Hydrogen bonds are key interactions determining protein-ligand binding affinity and therefore fundamental to any biological process. Unfortunately, explicit…”
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Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors by Gohlke, Holger, Klebe, Gerhard

“…The influence of a xenobiotic compound on an organism is usually summarized by the expression biological activity. If a controlled, therapeutically relevant,…”
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fconv: format conversion, manipulation and feature computation of molecular data by NEUDERT, Gerd, KLEBE, Gerhard

“…fconv is a program intended for parsing and manipulating multiple aspects and properties of molecular data. Up to now, it has been developed and extensively…”
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Role of Water Molecules in Protein–Ligand Dissociation and Selectivity Discrimination: Analysis of the Mechanisms and Kinetics of Biomolecular Solvation Using Molecular Dynamics by Hüfner-Wulsdorf, Tobias, Klebe, Gerhard

“…The mechanism by which water molecules modulate biomolecular interactions and the time scale of microscopic solvation processes are usually not known. This is…”
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Dissecting the Hydrophobic Effect on the Molecular Level: The Role of Water, Enthalpy, and Entropy in Ligand Binding to Thermolysin by Biela, Adam, Nasief, Nader N., Betz, Michael, Heine, Andreas, Hangauer, David, Klebe, Gerhard

“…The hydrophobic effect is associated with the successive replacement of water molecules in the binding site of a protein by hydrophobic groups of the ligand…”
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Ligand Binding Stepwise Disrupts Water Network in Thrombin: Enthalpic and Entropic Changes Reveal Classical Hydrophobic Effect by Biela, Adam, Sielaff, Frank, Terwesten, Felix, Heine, Andreas, Steinmetzer, Torsten, Klebe, Gerhard

“…Well-ordered water molecules are displaced from thrombin’s hydrophobic S3/4-pocket by P3-varied ligands (Gly, d-Ala, d-Val, d-Leu to d-Cha with increased…”
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Structure of Active Coagulation Factor XIII Triggered by Calcium Binding: Basis for the Design of Next-Generation Anticoagulants by Stieler, Martin, Weber, Johannes, Hils, Martin, Kolb, Peter, Heine, Andreas, Büchold, Christian, Pasternack, Ralf, Klebe, Gerhard

“…On active duty: The available drugs for cardiovascular diseases can promote blood clotting but can also lead to life‐threatening bleeding episodes. A promising…”
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Impact of Surface Water Layers on Protein–Ligand Binding: How Well Are Experimental Data Reproduced by Molecular Dynamics Simulations in a Thermolysin Test Case? by Betz, Michael, Wulsdorf, Tobias, Krimmer, Stefan G, Klebe, Gerhard

“…Drug binding involves changes of the local water structure around proteins including water rearrangements across surface-solvation layers around protein and…”
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A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology by Schmitt, Stefan, Kuhn, Daniel, Klebe, Gerhard

“…A new method has been developed to detect functional relationships among proteins independent of a given sequence or fold homology. It is based on the idea…”
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High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits by Schiebel, Johannes, Krimmer, Stefan G., Röwer, Karine, Knörlein, Anna, Wang, Xiaojie, Park, Ah Young, Stieler, Martin, Ehrmann, Frederik R., Fu, Kan, Radeva, Nedyalka, Krug, Michael, Huschmann, Franziska U., Glöckner, Steffen, Weiss, Manfred S., Mueller, Uwe, Klebe, Gerhard, Heine, Andreas

“…Today the identification of lead structures for drug development often starts from small fragment-like molecules raising the chances to find compounds that…”
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More than a Simple Lipophilic Contact: A Detailed Thermodynamic Analysis of Nonbasic Residues in the S1 Pocket of Thrombin by Baum, Bernhard, Mohamed, Menshawy, Zayed, Mohamed, Gerlach, Christof, Heine, Andreas, Hangauer, David, Klebe, Gerhard

“…The field of medicinal chemistry aims to design and optimize small molecule leads into drug candidates that may positively interfere with pathological disease…”
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Knowledge-based scoring function to predict protein-ligand interactions by Gohlke, Holger, Hendlich, Manfred, Klebe, Gerhard

“…The development and validation of a new knowledge-based scoring function (DrugScore) to describe the binding geometry of ligands in proteins is presented. It…”
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Successful Virtual Screening for a Submicromolar Antagonist of the Neurokinin-1 Receptor Based on a Ligand-Supported Homology Model by Evers, Andreas, Klebe, Gerhard

“…The neurokinin-1 (NK1) receptor belongs to the family of G-protein-coupled receptors (GPCRs), which represents one of the most relevant target families in…”
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A Proof-of-Concept Fragment Screening of a Hit-Validated 96-Compounds Library against Human Carbonic Anhydrase II by Glöckner, Steffen, Heine, Andreas, Klebe, Gerhard

“…Fragment screening is a powerful tool to identify and characterize binding pockets in proteins. We herein present the results of a proof-of-concept screening…”
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Molecular Docking Screens Using Comparative Models of Proteins by Fan, Hao, Irwin, John J, Webb, Benjamin M, Klebe, Gerhard, Shoichet, Brian K, Sali, Andrej

“…Two orders of magnitude more protein sequences can be modeled by comparative modeling than have been determined by X-ray crystallography and NMR spectroscopy…”
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Targeting the Blind Spot of Polycationic Nanocarrier-Based siRNA Delivery by Zheng, Mengyao, Pavan, Giovanni M, Neeb, Manuel, Schaper, Andreas K, Danani, Andrea, Klebe, Gerhard, Merkel, Olivia M, Kissel, Thomas

“…Polycationic nanocarriers attract increasing attention to the field of siRNA delivery. We investigated the self-assembly of siRNA vs pDNA with polycations,…”
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