Search Results - "GOHLKE, Holger"

Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method by Homeyer, Nadine, Gohlke, Holger

“…Detailed knowledge of how molecules recognize interaction partners and of the conformational preferences of biomacromolecules is pivotal for understanding…”
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Protein rigidity and thermophilic adaptation by Radestock, Sebastian, Gohlke, Holger

“…We probe the hypothesis of corresponding states, according to which homologues from mesophilic and thermophilic organisms are in corresponding states of…”
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FEW: A workflow tool for free energy calculations of ligand binding by Homeyer, Nadine, Gohlke, Holger

“…In the later stages of drug design projects, accurately predicting relative binding affinities of chemically similar compounds to a biomolecular target is of…”
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Structure and efflux mechanism of the yeast pleiotropic drug resistance transporter Pdr5 by Harris, Andrzej, Wagner, Manuel, Du, Dijun, Raschka, Stefanie, Nentwig, Lea-Marie, Gohlke, Holger, Smits, Sander H. J., Luisi, Ben F., Schmitt, Lutz

“…Pdr5, a member of the extensive ABC transporter superfamily, is representative of a clinically relevant subgroup involved in pleiotropic drug resistance. Pdr5…”
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Resolving dynamics and function of transient states in single enzyme molecules by Sanabria, Hugo, Rodnin, Dmitro, Hemmen, Katherina, Peulen, Thomas-Otavio, Felekyan, Suren, Fleissner, Mark R., Dimura, Mykola, Koberling, Felix, Kühnemuth, Ralf, Hubbell, Wayne, Gohlke, Holger, Seidel, Claus A. M.

“…We use a hybrid fluorescence spectroscopic toolkit to monitor T4 Lysozyme (T4L) in action by unraveling the kinetic and dynamic interplay of the conformational…”
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MMPBSA.py: An Efficient Program for End-State Free Energy Calculations by Miller, Bill R, McGee, T. Dwight, Swails, Jason M, Homeyer, Nadine, Gohlke, Holger, Roitberg, Adrian E

“…MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. MMPBSA.py is a program written in Python for streamlining…”
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A Novel Polyester Hydrolase From the Marine Bacterium Pseudomonas aestusnigri - Structural and Functional Insights by Bollinger, Alexander, Thies, Stephan, Knieps-Grünhagen, Esther, Gertzen, Christoph, Kobus, Stefanie, Höppner, Astrid, Ferrer, Manuel, Gohlke, Holger, Smits, Sander H J, Jaeger, Karl-Erich

“…Biodegradation of synthetic polymers, in particular polyethylene terephthalate (PET), is of great importance, since environmental pollution with PET and other…”
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On the contributing role of the transmembrane domain for subunit-specific sensitivity of integrin activation by Pagani, Giulia, Gohlke, Holger

“…Integrins are α/β heterodimeric transmembrane adhesion receptors. Evidence exists that their transmembrane domain (TMD) separates upon activation…”
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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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Quantitative assessment of the determinant structural differences between redox-active and inactive glutaredoxins by Liedgens, Linda, Zimmermann, Jannik, Wäschenbach, Lucas, Geissel, Fabian, Laporte, Hugo, Gohlke, Holger, Morgan, Bruce, Deponte, Marcel

“…Class I glutaredoxins are enzymatically active, glutathione-dependent oxidoreductases, whilst class II glutaredoxins are typically enzymatically inactive, Fe-S…”
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Automated and optimally FRET-assisted structural modeling by Dimura, Mykola, Peulen, Thomas-Otavio, Sanabria, Hugo, Rodnin, Dmitro, Hemmen, Katherina, Hanke, Christian A., Seidel, Claus A. M., Gohlke, Holger

“…FRET experiments can provide state-specific structural information of complex dynamic biomolecular assemblies. However, to overcome the sparsity of FRET…”
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A toolkit and benchmark study for FRET-restrained high-precision structural modeling by Kalinin, Stanislav, Peulen, Thomas, Sindbert, Simon, Rothwell, Paul J, Berger, Sylvia, Restle, Tobias, Goody, Roger S, Gohlke, Holger, Seidel, Claus A M

“…A collection of simulation tools and workflow for single-molecule Förster resonance energy transfer (smFRET) allows highly quantitative structural modeling…”
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Partially inserted nascent chain unzips the lateral gate of the Sec translocon by Kater, Lukas, Frieg, Benedikt, Berninghausen, Otto, Gohlke, Holger, Beckmann, Roland, Kedrov, Alexej

“…The Sec translocon provides the lipid bilayer entry for ribosome‐bound nascent chains and thus facilitates membrane protein biogenesis. Despite the appreciated…”
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Computational Analyses of the AtTPC1 (Arabidopsis Two-Pore Channel 1) Permeation Pathway by Navarro-Retamal, Carlos, Schott-Verdugo, Stephan, Gohlke, Holger, Dreyer, Ingo

“…Two Pore Channels (TPCs) are cation-selective voltage- and ligand-gated ion channels in membranes of intracellular organelles of eukaryotic cells. In plants,…”
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Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf by Gohlke, Holger, Case, David A.

“…Estimating protein–protein interaction energies is a very challenging task for current simulation protocols. Here, absolute binding free energies are reported…”
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Structural Rigidity and Protein Thermostability in Variants of Lipase A from Bacillus subtilis by Rathi, Prakash Chandra, Jaeger, Karl-Erich, Gohlke, Holger

“…Understanding the origin of thermostability is of fundamental importance in protein biochemistry. Opposing views on increased or decreased structural rigidity…”
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40 Years of Research on Polybrominated Diphenyl Ethers (PBDEs)-A Historical Overview and Newest Data of a Promising Anticancer Drug by Schmitt, Laura, Hinxlage, Ilka, Cea, Pablo A, Gohlke, Holger, Wesselborg, Sebastian

“…Polybrominated diphenyl ethers (PBDEs) are a group of molecules with an ambiguous background in literature. PBDEs were first isolated from marine sponges of…”
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Cosolvent-Enhanced Sampling and Unbiased Identification of Cryptic Pockets Suitable for Structure-Based Drug Design by Schmidt, Denis, Boehm, Markus, McClendon, Christopher L, Torella, Rubben, Gohlke, Holger

“…Modulating protein activity with small-molecules binding to cryptic pockets offers great opportunities to overcome hurdles in drug design. Cryptic sites are…”
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On the potential alternate binding change mechanism in a dimeric structure of Pyruvate Phosphate Dikinase by Ciupka, Daniel, Gohlke, Holger

“…The pyruvate phosphate dikinase (PPDK) reaction mechanism is characterized by a distinct spatial separation of reaction centers and large conformational…”
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Structural Model of the ETR1 Ethylene Receptor Transmembrane Sensor Domain by Schott-Verdugo, Stephan, Müller, Lena, Classen, Elisa, Gohlke, Holger, Groth, Georg

“…The structure, mechanism of action and copper stoichiometry of the transmembrane sensor domain of the plant ethylene receptor ETR1 and homologs have remained…”
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