Search Results - "Schaarschmidt, Joerg"

Assessment of contact predictions in CASP12: Co‐evolution and deep learning coming of age by Schaarschmidt, Joerg, Monastyrskyy, Bohdan, Kryshtafovych, Andriy, Bonvin, Alexandre M.J.J.

“…Following up on the encouraging results of residue‐residue contact prediction in the CASP11 experiment, we present the analysis of predictions submitted for…”
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SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots by Moreira, Irina S., Koukos, Panagiotis I., Melo, Rita, Almeida, Jose G., Preto, Antonio J., Schaarschmidt, Joerg, Trellet, Mikael, Gümüş, Zeynep H., Costa, Joaquim, Bonvin, Alexandre M. J. J.

“…We present SpotOn, a web server to identify and classify interfacial residues as Hot-Spots (HS) and Null-Spots (NS). SpotON implements a robust algorithm with…”
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Rearrangement of the Extracellular Domain/Extracellular Loop 1 Interface Is Critical for Thyrotropin Receptor Activation by Schaarschmidt, Joerg, Nagel, Marcus B.M., Huth, Sandra, Jaeschke, Holger, Moretti, Rocco, Hintze, Vera, von Bergen, Martin, Kalkhof, Stefan, Meiler, Jens, Paschke, Ralf

“…The thyroid stimulating hormone receptor (TSHR) is a G protein-coupled receptor (GPCR) with a characteristic large extracellular domain (ECD). TSHR activation…”
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An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action [version 2; peer review: 2 approved] by Anzt, Hartwig, Bach, Felix, Druskat, Stephan, Löffler, Frank, Loewe, Axel, Renard, Bernhard Y, Seemann, Gunnar, Struck, Alexander, Achhammer, Elke, Aggarwal, Piush, Appel, Franziska, Bader, Michael, Brusch, Lutz, Busse, Christian, Chourdakis, Gerasimos, Dabrowski, Piotr Wojciech, Ebert, Peter, Flemisch, Bernd, Friedl, Sven, Fritzsch, Bernadette, Funk, Maximilian D, Gast, Volker, Goth, Florian, Grad, Jean-Noël, Hegewald, Jan, Hermann, Sibylle, Hohmann, Florian, Janosch, Stephan, Kutra, Dominik, Linxweiler, Jan, Muth, Thilo, Peters-Kottig, Wolfgang, Rack, Fabian, Raters, Fabian H.C, Rave, Stephan, Reina, Guido, Reißig, Malte, Ropinski, Timo, Schaarschmidt, Joerg, Seibold, Heidi, Thiele, Jan P, Uekermann, Benjamin, Unger, Stefan, Weeber, Rudolf

“…Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research…”
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Natural helix 9 mutants of PPARγ differently affect its transcriptional activity by Broekema, Marjoleine F., Massink, Maarten P.G., Donato, Cinzia, de Ligt, Joep, Schaarschmidt, Joerg, Borgman, Anouska, Schooneman, Marieke G., Melchers, Diana, Gerding, Martin N., Houtman, René, Bonvin, Alexandre M.J.J., Majithia, Amit R., Monajemi, Houshang, van Haaften, Gijs W., Soeters, Maarten R., Kalkhoven, Eric

“…The nuclear receptor PPARγ is the master regulator of adipocyte differentiation, distribution, and function. In addition, PPARγ induces terminal…”
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Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server by Vangone, Anna, Schaarschmidt, Joerg, Koukos, Panagiotis, Geng, Cunliang, Citro, Nevia, Trellet, Mikael E, Xue, Li C, Bonvin, Alexandre M J J

“…Recently we published PROtein binDIng enerGY (PRODIGY), a web-server for the prediction of binding affinity in protein-protein complexes. By using a…”
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Cover Image, Volume 86, Issue S1 by Schaarschmidt, Joerg, Monastyrskyy, Bohdan, Kryshtafovych, Andriy, Bonvin, Alexandre M.J.J.

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Workflow Engineering in Materials Design within the BATTERY 2030+ Project by Schaarschmidt, Joerg, Yuan, Jie, Strunk, Timo, Kondov, Ivan, Huber, Sebastiaan P., Pizzi, Giovanni, Kahle, Leonid, Bölle, Felix T., Castelli, Ivano E., Vegge, Tejs, Hanke, Felix, Hickel, Tilmann, Neugebauer, Jörg, Rêgo, Celso R. C., Wenzel, Wolfgang

“…In recent years, modeling and simulation of materials have become indispensable to complement experiments in materials design. High‐throughput simulations…”
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The HADDOCK2.4 web server for integrative modeling of biomolecular complexes by Honorato, Rodrigo V., Trellet, Mikael E., Jiménez-García, Brian, Schaarschmidt, Jörg J., Giulini, Marco, Reys, Victor, Koukos, Panagiotis I., Rodrigues, João P. G. L. M., Karaca, Ezgi, van Zundert, Gydo C. P., Roel-Touris, Jorge, van Noort, Charlotte W., Jandová, Zuzana, Melquiond, Adrien S. J., Bonvin, Alexandre M. J. J.

“…Interactions between macromolecules, such as proteins and nucleic acids, are essential for cellular functions. Experimental methods can fail to provide all the…”
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Substrate specificity of the pyrophosphohydrolase LpxH determines the asymmetry of Bordetella pertussis lipid A by Arenas, Jesús, Pupo, Elder, de Jonge, Eline, Pérez-Ortega, Jesús, Schaarschmidt, Joerg, van der Ley, Peter, Tommassen, Jan

“…Lipopolysaccharides are anchored to the outer membrane of Gram-negative bacteria by a hydrophobic moiety known as lipid A, which potently activates the host…”
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A Newly Discovered TSHR Variant (L665F) Associated With Nonautoimmune Hyperthyroidism in an Austrian Family Induces Constitutive TSHR Activation by Steric Repulsion Between TM1 and TM7 by Jaeschke, Holger, Schaarschmidt, Joerg, Eszlinger, Markus, Huth, Sandra, Puttinger, Rudolf, Rittinger, Olaf, Meiler, Jens, Paschke, Ralf

“…Objective: New in vivo mutations in G protein-coupled receptors open opportunities for insights into the mechanism of receptor activation. Here we describe the…”
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Somatic mutations in 33 benign and malignant hot thyroid nodules in children and adolescents by Eszlinger, Markus, Niedziela, Marek, Typlt, Eva, Jaeschke, Holger, Huth, Sandra, Schaarschmidt, Jörg, Aigner, Thomas, Trejster, Ewa, Krohn, Knut, Bösenberg, Eileen, Paschke, Ralf

“…•Clinical and molecular data of hot thyroid nodules (HTNs) in children are rare.•We present clinical/molecular data for 33 consecutive (29 benign/4 malignant)…”
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Influence of the hinge region and its adjacent domains on binding and signaling patterns of the thyrotropin and follitropin receptor by Schaarschmidt, Jörg, Huth, Sandra, Meier, René, Paschke, Ralf, Jaeschke, Holger

“…Glycoprotein hormone receptors (GPHR) have a large extracellular domain (ECD) divided into the leucine rich repeat (LRR) domain for binding of the glycoprotein…”
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Shared metadata for data-centric materials science by Ghiringhelli, Luca M., Baldauf, Carsten, Bereau, Tristan, Brockhauser, Sandor, Carbogno, Christian, Chamanara, Javad, Cozzini, Stefano, Curtarolo, Stefano, Draxl, Claudia, Dwaraknath, Shyam, Fekete, Ádám, Kermode, James, Koch, Christoph T., Kühbach, Markus, Ladines, Alvin Noe, Lambrix, Patrick, Himmer, Maja-Olivia, Levchenko, Sergey V., Oliveira, Micael, Michalchuk, Adam, Miller, Ronald E., Onat, Berk, Pavone, Pasquale, Pizzi, Giovanni, Regler, Benjamin, Rignanese, Gian-Marco, Schaarschmidt, Jörg, Scheidgen, Markus, Schneidewind, Astrid, Sheveleva, Tatyana, Su, Chuanxun, Usvyat, Denis, Valsson, Omar, Wöll, Christof, Scheffler, Matthias

“…The expansive production of data in materials science, their widespread sharing and repurposing requires educated support and stewardship. In order to ensure…”
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The Hinge Region of the TSH Receptor Stabilizes Ligand Binding and Determines Different Signaling Profiles of Human and Bovine TSH by Jaeschke, Holger, Schaarschmidt, Jörg, Günther, Robert, Mueller, Sandra

“…The hinge region (HinR) is a variable structure of glycoprotein hormone receptors. Its amino acid composition and length is different for glycoprotein hormone…”
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Conversion of a decarboxylating to a non-decarboxylating glutaryl-coenzyme A dehydrogenase by site-directed mutagenesis by Schaarschmidt, Jörg, Wischgoll, Simon, Hofmann, Hans-Jörg, Boll, Matthias

“…Glutaryl-coenzyme A (CoA) dehydrogenases (GDHs) are acyl-CoA dehydrogenases, which usually dehydrogenate and decarboxylate the substrate to crotonyl-CoA. In…”
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Identification of Novel TSH Interaction Sites by Systematic Binding Analysis of the TSHR Hinge Region by Mueller, Sandra, Szkudlinski, Mariusz W, Schaarschmidt, Jörg, Günther, Robert, Paschke, Ralf, Jaeschke, Holger

“…In which ways the binding of the thyroid stimulating hormone to the extracellular domain of its receptor leads to activation of the thyroid-stimulating hormone…”
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An environment for sustainable research software in Germany and beyond: Current state, open challenges, and call for action by Anzt, Hartwig, Bach, Felix, Druskat, Stephan, Löffler, Frank, Loewe, Axel, Renard, Bernhard Y, Seemann, Gunnar, Struck, Alexander, Achhammer, Elke, Aggarwal, Piush, Appel, Franziska, Bader, Michael, Brusch, Lutz, Busse, Christian, Chourdakis, Gerasimos, Dabrowski, Piotr Wojciech, Ebert, Peter, Flemisch, Bernd, Friedl, Sven, Fritzsch, Bernadette, Funk, Maximilian D, Gast, Volker, Goth, Florian, Grad, Jean-Noël, Hermann, Sibylle, Hohmann, Florian, Janosch, Stephan, Kutra, Dominik, Linxweiler, Jan, Muth, Thilo, Peters-Kottig, Wolfgang, Rack, Fabian, Raters, Fabian H.C, Rave, Stephan, Reina, Guido, Reißig, Malte, Ropinski, Timo, Schaarschmidt, Joerg, Seibold, Heidi, Thiele, Jan P, Uekermann, Benjamin, Unger, Stefan, Weeber, Rudolf

“…Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research…”
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West-Life: A Virtual Research Environment for structural biology by Morris, Chris, Andreetto, Paolo, Banci, Lucia, Bonvin, Alexandre M.J.J., Chojnowski, Grzegorz, Cano, Laura del, Carazo, José Marıa, Conesa, Pablo, Daenke, Susan, Damaskos, George, Giachetti, Andrea, Haley, Natalie E.C., Hekkelman, Maarten L., Heuser, Philipp, Joosten, Robbie P., Kouřil, Daniel, Křenek, Aleš, Kulhánek, Tomáš, Lamzin, Victor S., Nadzirin, Nurul, Perrakis, Anastassis, Rosato, Antonio, Sanderson, Fiona, Segura, Joan, Schaarschmidt, Joerg, Sobolev, Egor, Traldi, Sergio, Trellet, Mikael E., Velankar, Sameer, Verlato, Marco, Winn, Martyn

“…[Display omitted] •Data processing and data management services for structural biology.•Enhancements to existing web services for structure solution and…”
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An Environment for Sustainable Research Software in Germany and Beyond: Current State, Open Challenges, and Call for Action by Anzt, Hartwig, Bach, Felix, Druskat, Stephan, Löffler, Frank, Loewe, Axel, Renard, Bernhard Y, Seemann, Gunnar, Struck, Alexander, Achhammer, Elke, Aggarwal, Piush, Appel, Franziska, Bader, Michael, Brusch, Lutz, Busse, Christian, Chourdakis, Gerasimos, Dabrowski, Piotr W, Ebert, Peter, Flemisch, Bernd, Friedl, Sven, Fritzsch, Bernadette, Funk, Maximilian D, Gast, Volker, Goth, Florian, Grad, Jean-Noël, Hermann, Sibylle, Hohmann, Florian, Janosch, Stephan, Kutra, Dominik, Linxweiler, Jan, Muth, Thilo, Peters-Kottig, Wolfgang, Rack, Fabian, Raters, Fabian H. C, Rave, Stephan, Reina, Guido, Reißig, Malte, Ropinski, Timo, Schaarschmidt, Joerg, Seibold, Heidi, Thiele, Jan P, Uekerman, Benjamin, Unger, Stefan, Weeber, Rudolf

“…F1000Research 2020 Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and…”
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