Items where Author is "Schwede, Torsten"

2017

Trewhella, Jill and Duff, Anthony P. and Durand, Dominique and Gabel, Frank and Guss, J. Mitchell and Hendrickson, Wayne A. and Hura, Greg L. and Jacques, David A. and Kirby, Nigel M. and Kwan, Ann H. and P`erez, Javier and Pollack, Lois and Ryan, Timothy M. and Sali, Andrej and Schneidman-Duhovny, Dina and Schwede, Torsten and Svergun, Dmitri I. and Sugiyama, Masaaki and Tainer, John A. and Vachette, Patrice and Westbrook, John and Whitten, Andrew E.. (2017) 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallographica Section D, 73 (9). pp. 710-728.

Romano, Valentina and de Beer, Tjaart A. P. and Schwede, Torsten. (2017) A computational protocol to evaluate the effects of protein mutants in the kinase gatekeeper position on the binding of ATP substrate analogues. BMC Research Notes, 10 (1). p. 104.

Thornton, Janet M. and Valencia, Alfonso and Schwede, Torsten. (2017) Anna Tramontano 1957-2017. Nature Structural and Molecular Biology, 24 (5). pp. 431-432.

Kryshtafovych, Andriy and Monastyrskyy, Bohdan and Fidelis, Krzysztof and Schwede, Torsten and Tramontano, Anna. (2017) Assessment of model accuracy estimations in CASP12. Proteins.

Sprecher, Kathrin S. and Hug, Isabelle and Nesper, Jutta and Potthoff, Eva and Mahi, Mohamed-Ali and Sangermani, Matteo and Kaever, Volkhard and Schwede, Torsten and Vorholt, Julia and Jenal, Urs. (2017) Cohesive Properties of the Caulobacter crescentus Holdfast Adhesin Are Regulated by a Novel c-di-GMP Effector Protein. mBio, 8 (2). e00294-17.

Daina, Antoine and Blatter, Marie-Claude and Baillie Gerritsen, Vivienne and Palagi, Patricia M. and Marek, Diana and Xenarios, Ioannis and Schwede, Torsten and Michielin, Olivier and Zoete, Vincent. (2017) Drug Design Workshop: A Web-Based Educational Tool To Introduce Computer-Aided Drug Design to the General Public. Journal of Chemical Education, 94 (3). pp. 335-344.

Heck, Angela and Milnik, Annette and Vukojevic, Vanja and Petrovska, Jana and Egli, Tobias and Singer, Jochen and Escobar, Pablo and Sengstag, Thierry and Coynel, David and Freytag, Virginie and Fastenrath, Matthias and Demougin, Philippe and Loos, Eva and Hartmann, Francina and Schicktanz, Nathalie and Delarue Bizzini, Bernardo and Vogler, Christian and Kolassa, Iris-Tatjana and Wilker, Sarah and Elbert, Thomas and Schwede, Torsten and Beisel, Christian and Beerenwinkel, Niko and de Quervain, Dominique J.-F. and Papassotiropoulos, Andreas. (2017) Exome sequencing of healthy phenotypic extremes links TROVE2 to emotional memory and PTSD. Nature Human Behaviour, 1. 0081.

Bertoni, Martino and Kiefer, Florian and Biasini, Marco and Bordoli, Lorenza and Schwede, Torsten. (2017) Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports, 7 (1). p. 10480.

Burley, Stephen K. and Kurisu, Genji and Markley, John L. and Nakamura, Haruki and Velankar, Sameer and Berman, Helen M. and Sali, Andrej and Schwede, Torsten and Trewhella, Jill. (2017) PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models. Structure , 25 (9). pp. 1317-1318.

Bienert, Stefan and Waterhouse, Andrew and de Beer, Tjaart A. P. and Tauriello, Gerardo and Studer, Gabriel and Bordoli, Lorenza and Schwede, Torsten. (2017) The SWISS-MODEL Repository - new features and functionality. Nucleic Acids Research, 45 (D1). D313-D319.

September 2016

Moult, John and Fidelis, Krzysztof and Kryshtafovych, Andriy and Schwede, Torsten and Tramontano, Anna. (2016) Critical assessment of methods of protein structure prediction (CASP) - progress and new directions in Round XI. Proteins, 84 (Suppl. 1). pp. 4-14.

2016

Moult, John and Fidelis, Krzysztof and Kryshtafovych, Andriy and Schwede, Torsten and Tramontano, Anna. (2016) Critical assessment of methods of protein structure prediction: Progress and new directions in round XI. Proteins: Structure, Function, and Bioinformatics , 84 (1). pp. 4-14.

Kryshtafovych, Andriy and Barbato, Alessandro and Monastyrskyy, Bohdan and Fidelis, Krzysztof and Schwede, Torsten and Tramontano, Anna. (2016) Methods of model accuracy estimation can help selecting the best models from decoy sets: assessment of model accuracy estimations in CASP11. Proteins: Structure, Function, and Bioinformatics , 84 (1). pp. 349-369.

Kryshtafovych, Andriy and Moult, John and Baslé, Arnaud and Burgin, Alex and Craig, Timothy K. and Edwards, Robert A. and Fass, Deborah and Hartmann, Marcus D. and Korycinski, Mateusz and Lewis, Richard J. and Lorimer, Donald and Lupas, Andrei N. and Newman, Janet and Peat, Thomas S. and Piepenbrink, Kurt H. and Prahlad, Janani and van Raaij, Mark J. and Rohwer, Forest and Segall, Anca M. and Seguritan, Victor and Sundberg, Eric J. and Singh, Abhimanyu K. and Wilson, Mark A. and Schwede, Torsten. (2016) Some of the most interesting CASP11 targets through the eyes of their authors. Proteins: Structure, Function, and Bioinformatics , 84 (1). pp. 34-50.

2015

Berman, Helen M. and Gabanyi, Margaret J. and Groom, Colin R. and Johnson, John E. and Murshudov, Garib N. and Nicholls, Robert A. and Reddy, Vijay and Schwede, Torsten and Zimmerman, Matthew D. and Westbrook, John and Minor, Wladek. (2015) Data to knowledge: how to get meaning from your result. IUCrJ, Vol. 2, H. 1. pp. 45-58.

Ihssen, Julian and Haas, Jürgen and Kowarik, Michael and Wiesli, Luzia and Wacker, Michael and Schwede, Torsten and Thöny-Meyer, Linda. (2015) Increased efficiency of Campylobacter jejuni N-oligosaccharyltransferase PglB by structure-guided engineering. Open biology, Vol. 5, H. 4 , 140227.

Sali, Andrej and Berman, Helen M. and Schwede, Torsten and Trewhella, Jill and Kleywegt, Gerard and Burley, Stephen K. and Markley, John and Nakamura, Haruki and Adams, Paul and Bonvin, Alexandre M. J. J. and Chiu, Wah and Peraro, Matteo Dal and Di Maio, Frank and Ferrin, Thomas E. and Grünewald, Kay and Gutmanas, Aleksandras and Henderson, Richard and Hummer, Gerhard and Iwasaki, Kenji and Johnson, Graham and Lawson, Catherine L. and Meiler, Jens and Marti-Renom, Marc A. and Montelione, Gaetano T. and Nilges, Michael and Nussinov, Ruth and Patwardhan, Ardan and Rappsilber, Juri and Read, Randy J. and Saibil, Helen and Schröder, Gunnar F. and Schwieters, Charles D. and Seidel, Claus A. M. and Svergun, Dmitri and Topf, Maya and Ulrich, Eldon L. and Velankar, Sameer and Westbrook, John D.. (2015) Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure: with folding and design, Vol. 23, H. 7. pp. 1156-1167.

March 2014

Haas, Jürgen and Schwede, Torsten. (2014) Unabhängige Validierung von Methoden zur Proteinstrukturvorhersage. Biospektrum, 20 (2). pp. 236-237.

2014

Studer, Gabriel and Biasini, Marco and Schwede, Torsten. (2014) Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane). Bioinformatics, Vol. 30, H. 17 , i505-i511.

Cassarino, Tiziano Gallo and Bordoli, Lorenza and Schwede, Torsten. (2014) Assessment of ligand binding site predictions in CASP10. Proteins, Vol. 82, Suppl. 2. pp. 154-163.

Kryshtafovych, Andriy and Barbato, Alessandro and Fidelis, Krzysztof and Monastyrskyy, Bohdan and Schwede, Torsten and Tramontano, Anna. (2014) Assessment of the assessment : evaluation of the model quality estimates in CASP10. Proteins, Vol. 82, Suppl. S2. pp. 112-126.

Kryshtafovych, Andriy and Moult, John and Bales, Patrick and Bazan, J. Fernando and Biasini, Marco and Burgin, Alex and Chen, Chen and Cochran, Frank V. and Craig, Timothy K. and Das, Rhiju and Fass, Deborah and Garcia-Doval, Carmela and Herzberg, Osnat and Lorimer, Donald and Luecke, Hartmut and Ma, Xiaolei and Nelson, Daniel C. and van Raaij, Mark J. and Rohwer, Forest and Segall, Anca and Seguritan, Victor and Zeth, Kornelius and Schwede, Torsten. (2014) Challenging the state-of-the-art in protein structure prediction : highlights of experimental target structures for the 10(th) Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Proteins, Vol. 82, Suppl. S2. pp. 26-42.

Schmidt, Tobias B. and Schwede, Torsten and Meuwly, Markus. (2014) Computational Analysis of Methyltransfer Reactions in Dengue Virus Methyltransferase. Journal of Physical Chemistry B, 118 (22). pp. 5882-5890.

Moult, John and Fidelis, Krzysztof and Kryshtafovych, Andriy and Schwede, Torsten and Tramontano, Anna. (2014) Critical assessment of methods of protein structure prediction (CASP) - round X. Proteins, Vol. 82, Suppl. S2 , S. 1–6.

Stockinger, Heinz and Altenhoff, Adrian M. and Arnold, Konstantin and Bairoch, Amos and Bastian, Frederic and Bergmann, Sven and Bougueleret, Lydie and Bucher, Philipp and Delorenzi, Mauro and Lane, Lydie and Mercier, Philippe Le and Lisacek, Frédérique and Michielin, Olivier and Palagi, Patricia M. and Rougemont, Jacques and Schwede, Torsten and Mering, Christian von and Nimwegen, Erik van and Walther, Daniel and Xenarios, Ioannis and Zavolan, Mihaela and Zdobnov, Evgeny M. and Zoete, Vincent and Appel, Ron D.. (2014) Fifteen years SIB Swiss Institute of Bioinformatics : life science databases, tools and support. Nucleic Acids Research, 42 (W1). W436-W441.

Schmidt, Tobias and Bergner, Andreas and Schwede, Torsten. (2014) Modelling three-dimensional protein structures for applications in drug design. Drug discovery today, Vol. 19, H. 7. pp. 890-897.

Biasini, Marco and Bienert, Stefan and Waterhouse, Andrew and Arnold, Konstantin and Studer, Gabriel and Schmidt, Tobias and Kiefer, Florian and Cassarino, Tiziano Gallo and Bertoni, Martino and Bordoli, Lorenza and Schwede, Torsten. (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42 (W1). W252-W258.

Uda, Narasimha Rao and Upert, Grégory and Angelici, Gaetano and Nicolet, Stefan and Schmidt, Tobias and Schwede, Torsten and Creus, Marc. (2014) Zinc-selective inhibition of the promiscuous bacterial amide-hydrolase DapE : implications of metal heterogeneity for evolution and antibiotic drug design. Metallomics, Vol. 6, H. 1. pp. 88-95.

2013

Schwede, Torsten. (2013) Homology Modeling of Protein Structures. In: Encyclopedia of Biophysics. Berlin, pp. 992-998.

Biasini, Marco and Schmidt, Tobias and Bienert, Stefan. and Mariani, Valerio and Studer, Gabriel and Haas, Juergen and Johner, Niklaus and Schenk, Andreas D. and Philippsen, Ansgar and Schwede, Torsten. (2013) OpenStructure : an integrated software framework for computational structural biology. Acta crystallographica. Section D, Biological crystallography, Vol. 69, Pt. 5. pp. 701-709.

Schwede, Torsten. (2013) Protein modeling: what happened to the "protein structure gap"? Structure: with folding and design, Vol. 21, H. 9. pp. 1531-1540.

Trewhella, Jill and Hendrickson, Wayne A. and Kleywegt, Gerard J. and Sali, Andrej and Sato, Mamoru and Schwede, Torsten and Svergun, Dmitri I. and Tainer, John A. and Westbrook, John and Berman, Helen M.. (2013) Report of the wwPDB Small-Angle Scattering Task Force : data requirements for biomolecular modeling and the PDB. Structure: with folding and design, Vol. 21, H. 6. pp. 875-881.

Haas, Juergen and Roth, Steven and Arnold, Konstantin and Kiefer, Florian and Schmidt, Tobias and Bordoli, Lorenza and Schwede, Torsten. (2013) The Protein Model Portal: a comprehensive resource for protein structure and model information. Database, 2013, bat031.

Mariani, Valerio and Biasini, Marco and Barbato, Alessandro and Schwede, Torsten. (2013) lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics, Vol. 29, H. 21. pp. 2722-2728.

1 April 2012

Barbato, Alessandro and Benkert, Pascal and Schwede, Torsten and Tramontano, Anna and Kosinski, Jan. (2012) Improving your target-template alignment with MODalign. Bioinformatics, 28 (7). pp. 1038-1039.

2012

Bordoli, Lorenza and Schwede, Torsten. (2012) Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal. In: Homology Modeling: Methods and Protocols, Vol. 857. New York, USA, pp. 107-136.

Schwede, Torsten and Iber, Dagmar. (2012) ECCB 2012 : The 11th European Conference on Computational Biology. Bioinformatics, Vol. 28, H. 18 , i303-i305.

2011

Schmidt, Tobias and Haas, Jürgen and Cassarino, Tiziano Gallo and Schwede, Torsten. (2011) Assessment of ligand-binding residue predictions in CASP9. Proteins, Vol. 79, H. 10. pp. 126-136.

Mariani, Valerio and Kiefer, Florian and Schmidt, Tobias and Haas, Juergen and Schwede, Torsten. (2011) Assessment of template based protein structure predictions in CASP9. Proteins, Vol. 79, H. 10. pp. 37-58.

Kinch, Lisa N. and Shi, Shuoyong and Cheng, Hua and Cong, Qian and Pei, Jimin and Mariani, Valerio and Schwede, Torsten and Grishin, Nick V.. (2011) CASP9 target classification. Proteins, Vol. 79, H. 10. pp. 21-36.

Kryshtafovych, Andriy and Moult, John and Bartual, Sergio G. and Bazan, J. Fernando and Berman, Helen and Casteel, Darren E. and Christodoulou, Evangelos and Everett, John K. and Hausmann, Jens and Heidebrecht, Tatjana and Hills, Tanya and Hui, Raymond and Hunt, John F. and Seetharaman, Jayaraman and Joachimiak, Andrzej and Kennedy, Michael A. and Kim, Choel and Lingel, Andreas and Michalska, Karolina and Montelione, Gaetano T. and Otero, José M. and Perrakis, Anastassis and Pizarro, Juan C. and van Raaij, Mark J. and Ramelot, Theresa A. and Rousseau, Francois and Tong, Liang and Wernimont, Amy K. and Young, Jasmine and Schwede, Torsten. (2011) Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Proteins: Structure, Function, and Bioinformatics , 79 (S10). pp. 6-20.

2006

Berman, Helen M. and Burley, Stephen K. and Chiu, Wah and Sali, Andrej and Adzhubei, Alexei and Bourne, Philip E. and Bryant, Stephen H. and Dunbrack, Roland L. and Fidelis, Krzysztof and Frank, Joachim and Godzik, Adam and Henrick, Kim and Joachimiak, Andrzej and Heymann, Bernard and Jones, David and Markley, John L. and Moult, John and Montelione, Gaetano T. and Orengo, Christine and Rossmann, Michael G. and Rost, Burkhard and Saibil, Helen and Schwede, Torsten and Standley, Daron M. and Westbrook, John D.. (2006) Outcome of a workshop on archiving structural models of biological macromolecules. Structure: with folding and design, Vol. 14, H. 8. pp. 1211-1217.

2002

Guex, Nicolas and Schwede, Torsten and Peitsch, Manuel C.. (2002) Imaging science in biochemistry. In: Encyclopedia of imaging science and technology. New York.