Items where Division is "05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (Schwede)"

2017

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.

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.

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.

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.

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

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.

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.

Starek, Greg and Freites, J. Alfredo and Bernèche, Simon and Tobias, Douglas J.. (2017) Gating energetics of a voltage-dependent K(+) channel pore domain. Journal of Computational Chemistry, 38 (16). pp. 1472-1478.

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

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.

Vullo, Sabrina and Bonifacio, Gaetano and Roy, Sophie and Johner, Niklaus and Bernèche, Simon and Kellenberger, Stephan. (2017) Conformational dynamics and role of the acidic pocket in ASIC pH-dependent gating. Proceedings of the National Academy of Sciences of the United States of America, 114 (14). pp. 3768-3773.

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.

4 January 2016

Swiss Institute of Bioinformatics Members, SIB. (2016) The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic acids research, 44 (D1). D27-D37.

2016

Auffray, Charles and Balling, Rudi and Barroso, Inês and Bencze, László and Benson, Mikael and Bergeron, Jay and Bernal-Delgado, Enrique and Blomberg, Niklas and Bock, Christoph and Conesa, Ana and Del Signore, Susanna and Delogne, Christophe and Devilee, Peter and Di Meglio, Alberto and Eijkemans, Marinus and Flicek, Paul and Graf, Norbert and Grimm, Vera and Guchelaar, Henk-Jan and Guo, Yi-Ke and Gut, Ivo Glynne and Hanbury, Allan and Hanif, Shahid and Hilgers, Ralf-Dieter and Honrado, Ángel and Hose, D. Rod and Houwing-Duistermaat, Jeanine and Hubbard, Tim and Janacek, Sophie Helen and Karanikas, Haralampos and Kievits, Tim and Kohler, Manfred and Kremer, Andreas and Lanfear, Jerry and Lengauer, Thomas and Maes, Edith and Meert, Theo and Müller, Werner and Nickel, Dörthe and Oledzki, Peter and Pedersen, Bertrand and Petkovic, Milan and Pliakos, Konstantinos and Rattray, Magnus and I. Màs, Josep Redón and Schneider, Reinhard and Sengstag, Thierry and Serra-Picamal, Xavier and Spek, Wouter and Vaas, Lea A. I. and van Batenburg, Okker and Vandelaer, Marc and Varnai, Peter and Villoslada, Pablo and Vizcaíno, Juan Antonio and Wubbe, John Peter Mary and Zanetti, Gianluigi. (2016) Making sense of big data in health research: Towards an EU action plan. Genome medicine, 8 (1). p. 71.

Bertoni, Martino. Modeling homo- and hetero-oligomers using in silico prediction of protein quaternary structure. 2016, Doctoral Thesis, University of Basel, Faculty of Science.

Bignucolo, Olivier Daniel. From peptides to transmembrane proteins : helix versus kink formations in highly dynamical systems. 2016, Doctoral Thesis, University of Basel, Faculty of Science.

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.

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.

Romano, Valentina. Computational engineering of co-substrate specificity in protein kinases. 2016, Doctoral Thesis, University of Basel, Faculty of Science.

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.

Uda, Narasimha Rao. Promiscuous behaviour of the bacterial metallohydrolase DapE : an evolutionary and mechanistic perspective. 2015, Doctoral Thesis, University of Basel, Faculty of Science.

March 2014

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

2014

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.

Cassarino, Tiziano Gallo. Modelling cofactors in comparative protein structure models by evolutionary inference. 2014, Doctoral Thesis, University of Basel, Faculty of Science.

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.

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.

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.

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.

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.

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.

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.

Wojtas-Niziurski, Wojciech. Study of molecular processes through calculation of multidimensional free energy landscapes. 2014, Doctoral Thesis, University of Basel, Faculty of Science.

Xu, Yanyan. Molecular mechanics investigation of the transport mechanisms in the CIC-ec1 H+/CI⁻ exchanger and P-glycoprotein/Sav1866 ABC transporter. 2014, Doctoral Thesis, University of Basel, Faculty of Science.

2013

Biasini, Marco. Accurate modeling of protein structures by homology. 2013, Doctoral Thesis, University of Basel, Faculty of Science.

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.

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.

Schmidt, Tobias Benjamin. Computational approaches for investigating protein-ligand interactions - towards an in-depth understanding of the dengue virus methyltransferase. 2013, Doctoral Thesis, University of Basel, Faculty of Science.

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

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.

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.

Kiefer, Florian. Modeling of tertiary and quaternary protein structures by homology. 2012, Doctoral Thesis, University of Basel, Faculty of Science.

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

2011

Baud, O. and Etter, S. and Spreafico, M. and Bordoli, L. and Schwede, T. and Vogel, H. and Pick, H. M.. (2011) The Mouse Eugenol Odorant Receptor : Structural and Functional Plasticity of a Broadly Tuned Odorant Binding Pocket. Biochemistry, Vol. 50, H. 5. pp. 843-853.

Benkert, P. and Biasini, M. and Schwede, T.. (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, Vol. 27, H. 3. pp. 343-350.

Gabanyi, M. J. and Adams, P. D. and Arnold, K. and Bordoli, L. and Carter, L. G. and Flippen-Andersen, J. and Gifford, L. and Haas, J. and Kouranov, A. and McLaughlin, W. A. and Micallef, D. I. and Minor, W. and Shah, R. and Schwede, T. and Tao, Y. P. and Westbrook, J. D. and Zimmerman, M. and Berman, H. M.. (2011) The Structural Biology Knowledgebase : a portal to protein structures, sequences, functions, and methods. Journal of structural and functional genomics, Vol. 12, H. 2. pp. 45-54.

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.

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.

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.

2010

Biasini, M. and Mariani, V. and Haas, J. and Scheuber, S. and Schenk, AD. and Schwede, T. and Philippsen, A.. (2010) OpenStructur : a flexible software framework for computational structural biology. Bioinformatics, Vol. 26. pp. 2626-2628.

Haas, J. and Schwede, T.. (2010) Protein Homology Modelling - Providing Three-dimensional Models for Proteins where Experimental Data is Missing. ERCIM News, Vol. 82. pp. 20-21.

Podvinec, M. and Lim, S. P. and Schmidt, T. B. and Scarsi, M. and Wen, D. and Sonntag, L. S. and Sanschagrin, P. and Shenkin, P. S. and Schwede, T.. (2010) Novel Inhibitors of Dengue Virus Methyltransferase : discovery by in vitro-driven virtual screening on a Desktop Computer Grid. Journal of Medicinal Chemistry, Vol. 53, H. 4. pp. 1483-1495.

Thorsteinsdottir, Holmfridur B.. Computational analysis of protein-ligand binding : from single continuous trajectories to multiple parallel simulations. 2010, Doctoral Thesis, University of Basel, Faculty of Science.

2009

Arnold, K. and Kiefer, F. and Kopp, J. and Battey, J. N. and Podvinec, M. and Westbrook, J. D. and Berman, H. M. and Bordoli, L. and Schwede, T.. (2009) The protein model portal. Journal of structural and functional genomics, 10 (1). pp. 1-8.

Battey, James Nicolas Duncan. Modelling the effects of single point mutations on the structure and function of proteins. 2009, Doctoral Thesis, University of Basel, Faculty of Science.

Benkert, P. and Kunzli, M. and Schwede, T.. (2009) QMEAN server for protein model quality estimation. Nucleic Acids Research, 37 (2 Supplement). W510-W514.

Benkert, P. and Schwede, T. and Tosatto, S. C.. (2009) QMEANclust : estimation of protein model quality by combining a composite scoring function with structural density information. BMC Structural Biology, Vol. 9 , 35.

Benkert, P. and Tosatto, S. C. and Schwede, T.. (2009) Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins, Vol. 77, H. S9. pp. 173-180.

Berman, H. M. and Westbrook, J. D. and Gabanyi, M. J. and Tao, W. and Shah, R. and Kouranov, A. and Schwede, T. and Arnold, K. and Kiefer, F. and Bordoli, L. and Kopp, J. and Podvinec, M. and Adams, P. D. and Carter, L. G. and Minor, W. and Nair, R. and Baer, J. L.. (2009) The protein structure initiative structural genomics knowledgebase. Nucleic Acids Research, 37 (1 Supplement). D365-D368.

Bordoli, L. and Kiefer, F. and Arnold, K. and Benkert, P. and Battey, J. and Schwede, T.. (2009) Protein structure homology modelling using SWISS-MODEL Workspace. Nature Protocols, Vol. 4, H. 1. pp. 1-13.

Duerig, A. and Abel, S. and Folcher, M. and Nicollier, M. and Schwede, T. and Amiot, N. and Giese, B. and Jenal, U.. (2009) Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression. Genes & development, Vol. 23, H. 1. pp. 93-104.

Guex, N. and Peitsch, M. C. and Schwede, T.. (2009) Automated comparative protein structure modeling with Swiss-model and Swiss-PdbViewer : a historical perspective. Electrophoresis, Vol. 30, H. S1. pp. 162-173.

Kiefer, F. and Arnold, K. and Kunzli, M. and Bordoli, L. and Schwede, T.. (2009) The Swiss-model Repository and associated resources. Nucleic Acids Research, 37 (1 Supplement). D387-D392.

Pick, H. and Etter, S. and Baud, O. and Schmauder, R. and Bordoli, L. and Schwede, T. and Vogel, H.. (2009) Dual activities of odorants on olfactory and nuclear hormone receptors. Journal of biological chemistry, Vol. 284, H. 44. pp. 30547-30555.

Schwede, T. and Peitsch, M. C.. (2009) Protein Structure Modeling and Docking at the Swiss Institute of Bioinformatics. In: Bioinformatics. A Swiss Perspective. New Jersey, pp. 219-246.

Schwede, T. and Sali, A. and Honig, B. and Levitt, M. and Berman, H. M. and Jones, D. and Brenner, S. E. and Burley, S. K. and Das, R. and Dokholyan, N. V. and Dunbrack, R. L. J. and Fidelis, K. and Fiser, A. and Godzik, A. and Huang, Y. J. and Humblet, C. and Jacobson, M. P. and Joachimiak, A. and Krystek, S. R. J. and Kortemme, T. and Kryshtafovych, A. and Montelione, G. T. and Moult, J. and Murray, D. and Sanchez, R. and Sosnick, T. R. and Standley, D. M. and Stouch, T. and Vajda, S. and Vasquez, M. and Westbrook, J. D. and Wilson, I. A.. (2009) Outcome of a workshop on applications of protein models in biomedical research. Structure, Vol. 17, H. 2. pp. 151-159.

2008

Podvinec, M. and Schwede, T. and Peitsch, M. C.. (2008) Docking for neglected diseases as community efforts. In: Computational structural biology. Singapore, pp. 683-704.

Schwede, T. and Sali, A. and Eswar, N. and Peitsch, M. C.. (2008) Protein Structure Modeling. In: Computational structural biology. Singapore, p. 700.

2007

Battey, J. N. D. and Kopp, J. and Bordoli, L. and Read, R. J. and Clarke, N. D. and Schwede, T.. (2007) Automated server predictions in CASP7. Proteins, Vol. 69 Suppl 8. pp. 68-82.

Bordoli, L. and Kiefer, F. and Schwede, T.. (2007) Assessment of disorder predictions in CASP7. Proteins, Vol. 69 Suppl 8. pp. 129-136.

Clarke, N. D. and Ezkurdia, I. and Kopp, J. and Read, R. J. and Schwede, T. and Tress, M.. (2007) Domain Definition and Target Classification for CASP7. Proteins, Vol. 69, H. S8. pp. 10-18.

Junne, T. and Schwede, T. and Goder, V. and Spiess, M.. (2007) Mutations in the Sec61p channel affecting signal sequence recognition and membrane protein topology. Journal of biological chemistry, Vol. 282, H. 45. pp. 33201-33209.

Kopp, J. and Bordoli, L. and Battey, J. N. D. and Kiefer, F. and Schwede, T.. (2007) Assessment of CASP7 predictions for template-based modeling targets. Proteins, Vol. 69 Suppl 8. pp. 38-56.

Michelsen, K. and Schmid, V. and Metz, J. and Heusser, K. and Liebel, U. and Schwede, T. and Spang, A. and Schwappach, B.. (2007) Novel cargo-binding site in the beta and delta subunits of coatomer. The Journal of cell biology, Vol. 179, H. 2. pp. 209-217.

Scarsi, M. and Podvinec, M. and Roth, A. and Hug, H. and Kersten, S. and Albrecht, H. and Schwede, T. and Meyer, U. A. and Rucker, C.. (2007) Sulfonylureas and glinides exhibit peroxisome proliferator-activated receptor gamma activity : a combined virtual screening and biological assay approach. Molecular pharmacology, Vol. 71, H. 2. pp. 398-406.

Zosso, D. and Arnold, K. and Schwede, T. and Podvinec, M.. (2007) SWISS-TANDEM : a Web-based workspace for MS/MS protein identification on PC grid. In: Twentieth IEEE international symposium on computer-based medical systems, CBMS 2007. Los Alamitos, Calif., pp. 406-411.

Zosso, D. and Podvinec, M. and Muller, M. and Aebersold, R. and Peitsch, M. C. and Schwede, T.. (2007) Tandem mass spectrometry protein identification on a PC grid. Studies in health technology and informatics, Vol. 126. pp. 3-12.

2006

Arnold, K. and Bordoli, L. and Kopp, J. and Schwede, T.. (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics, Vol. 22, H. 2. pp. 195-201.

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.

Di Scala, Franck. Untersuchung von Muskelgewebe amyotorpher lateraler Sklerose : Etiologie, Diagnose und therapeutische Aspekte. 2006, Doctoral Thesis, University of Basel, Faculty of Science.

Junne, T. and Schwede, T. and Goder, V. and Spiess, M.. (2006) The plug domain of yeast Sec61p is important for efficient protein translocation, but is not essential for cell viability. Molecular Biology of the Cell, 17 (9). pp. 4063-4068.

Kopp, J. and Schwede, T.. (2006) The Swiss-model Repository : new features and functionalities. Nucleic Acids Research, 34 (D1). D315-D318.

Podvinec, M. and Maffioletti, S. and Kunszt, P. and Arnold, K. and Cerutti, L. and Nyffeler, B. and Schlapbach, R. and Turker, C. and Stockinger, H. and Thomas, A. J. and Peitsch, M. C. and Schwede, T.. (2006) The SwissBioGrid Project : objectives, preliminary results and lessons learned. In: e-Science 2006 : 2nd IEEE International Conference on e-Science and Grid Computing, e-Science 2006, 148. Los Alamitos, Calif..

Schlecht, Ulrich. Analysis of the transcriptional program governing meiosis and gametogenesis in yeast and mammals. 2006, Doctoral Thesis, University of Basel, Faculty of Science.

Thorsteinsdottir, H. B. and Schwede, T. and Zoete, V. and Meuwly, M.. (2006) How inaccuracies in protein structure models affect estimates of protein-ligand interactions : computational analysis of HIV-I protease inhibitor binding. Proteins, 65 (2). pp. 407-423.

2005

Monigatti, Flavio. Algorithms for the analysis of MALDI peptide mass fingerprint spectra for proteomics. 2005, Doctoral Thesis, University of Basel, Faculty of Science.

2004

Kopp, J. and Schwede, T.. (2004) Automated protein structure homology modeling : a progress report. Pharmacogenomics, Vol. 5, H. 4. pp. 405-416.

Kopp, J. and Schwede, T.. (2004) The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. Nucleic Acids Research, 32 (1 Supplement). D230-D234.

2003

Deutsch, S. and Rideau, A. and Bochaton-Piallat, M. and Merla, G. and Geinoz, A. and Gabbiani, G. and Schwede, T. and Matthes, T. and Antonarakis, S. E. and Beris, P.. (2003) Asp1424Asn MYH9 mutation results in an unstable protein responsible for the phenotypes in May-Hegglin anomaly/Fechtner syndrome. Blood, Vol. 102. pp. 529-534.

Fritzsche, H. B. and Schwede, T. and Schulz, G. E.. (2003) Covalent and three-dimensional structure of the cyclodextrinase from Flavobacterium sp. no. 92. European journal of biochemistry, Vol. 270, H. 10. pp. 2332-2341.

Schwede, T. and Kopp, J. and Guex, N. and Peitsch, M. C.. (2003) Swiss-model : an automated protein homology-modeling server. Nucleic Acids Research, 31 (13). pp. 3381-3385.

2002

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

Kopp, J. and Peitsch, M. C. and Schwede, T.. (2002) Protein Structure Modeling in Functional Genomics. In: Frontiers in Computational Genomics. Horizon Scientific Press.

Peitsch, M. C. and Schwede, T. and Diemand, A. and Guex, N.. (2002) Protein homology modeling. Nature encyclopedia of the human genome, Vol. 4.

Wattenhofer, M. and Di Iorio, M. V. and Rabionet, R. and Dougherty, L. and Pampanos, A. and Schwede, T. and Montserrat-Sentis, B. and Arbones, M. L. and Iliades, T. and Pasquadibisceglie, A. and D'Amelio, M. and Alwan, S. and Rossier, C. and Dahl, H. H. M. and Petersen, M. B. and Estivill, X. and Gasparini, P. and Scott, H. S. and Antonarakis, S. E.. (2002) Mutations in the TMPRSS3 gene are a rare cause of childhood non-syndromic deafness in Caucasian patients. Journal of molecular medicine, Vol. 80. pp. 124-131.

2001

Masmoudi, S. and Antonarakis, S. E. and Schwede, T. and Ghorbel, A. M. and Gratri, M. and Pappasavas, M. P. and Drira, M. and Elgaied Boulila, A. and Wattenhofer, M. and Rossier, C. and Scott, H. S. and Ayadi, H. and Guipponi, M.. (2001) Novel missense mutations of TMPRSS3 in two consanguineous Tunisian families with non-syndromic autosomal recessive deafness. Human mutation, Vol. 18, no. 2. pp. 101-108.

2000

Guex, N. and Schwede, T. and Peitsch, M. C.. (2000) Protein Tertiary Structure Modeling. In: Current Protocols in Protein Science, nit 2.8.1-2.8.17. [New York].

Peitsch, M. C. and Schwede, T. and Guex, N.. (2000) Automated protein modelling-the proteome in 3D. Pharmacogenomics, Vol. 1, no. 3. pp. 257-266.

Schwede, T. and Diemand, A. and Guex, N. and Peitsch, M. C.. (2000) Protein structure computing in the genomic era. Research in microbiology, Vol. 151. pp. 107-112.

1999

Schwede, T. F. and Badeker, M. and Langer, M. and Retey, J. and Schulz, G. E.. (1999) Homogenization and Crystallization of Histidine Ammonia-Lyase by Exchange of a Surface Cysteine Residue. Protein Engineering, 12 (2). pp. 151-153.

Schwede, T. F. and Retey, J. and Schulz, G. E.. (1999) Crystal Structure of Histidine Ammonia-Lyase Revealing a Novel Polypeptide Modification as the Catalytic Electrophile. Biochemistry, 38 (17). pp. 5355-5361.

1994

Wach, A. and Brachat, A. and Pöhlmann, R. and Philippsen, P.. (1994) New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast, Vol. 10, H. 13. pp. 1793-1808.