2020
Gervasoni, Silvia;
Vistoli, Giulio;
Talarico, Carmine;
Manelfi, Candida;
Beccari, Andrea R;
Studer, Gabriel;
Tauriello, Gerardo;
Waterhouse, Andrew Mark;
Schwede, Torsten;
Pedretti, Alessandro (2020).
A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0. International journal of molecular sciences, 21 (14), 5152.
Coman Schmid, Diana;
Crameri, Katrin;
Oesterle, Sabine;
Rinn, Bernd;
Sengstag, Thierry;
Stockinger, Heinz;
BioMedIT network team, (2020).
SPHN - The BioMedIT Network: A Secure IT Platform for Research with Sensitive Human Data. Studies in health technology and informatics, 270, 1170-1174.
Righetto, Ricardo D;
Anton, Leonie;
Adaixo, Ricardo;
Jakob, Roman P;
Zivanov, Jasenko;
Mahi, Mohamed-Ali;
Ringler, Philippe;
Schwede, Torsten;
Maier, Timm;
Stahlberg, Henning;
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High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica. , bioRxiv. . , 2020.04.28.065599.
2019
Berman, Helen M.;
Adams, Paul D.;
Bonvin, Alexandre A.;
Burley, Stephen K.;
Carragher, Bridget;
Chiu, Wah;
DiMaio, Frank;
Ferrin, Thomas E.;
Gabanyi, Margaret J.;
Goddard, Thomas D.;
Griffin, Patrick R.;
Haas, Juergen;
Hanke, Christian A.;
Hoch, Jeffrey C.;
Hummer, Gerhard;
Kurisu, Genji;
Lawson, Catherine L.;
Leitner, Alexander;
Markley, John L.;
Meiler, Jens;
Montelione, Gaetano T.;
Phillips, George N.;
Prisner, Thomas;
Rappsilber, Juri;
Schriemer, David C.;
Schwede, Torsten;
Seidel, Claus A. M.;
Strutzenberg, Timothy S.;
Svergun, Dmitri I.;
Tajkhorshid, Emad;
Trewhella, Jill;
Vallat, Brinda;
Velankar, Sameer;
Vuister, Geerten W.;
Webb, Benjamin;
Westbrook, John D.;
White, Kate L.;
Sali, Andrej (2019).
Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure (London, England : 1993), 27 (12), 1745-1759.
Kryshtafovych, Andriy;
Schwede, Torsten;
Topf, Maya;
Fidelis, Krzysztof;
Moult, John (2019).
Critical assessment of methods of protein structure prediction (CASP)-Round XIII. Proteins, 87 (12), 1011-1020.
Haas, Juergen;
Gumienny, Rafal;
Barbato, Alessandro;
Ackermann, Flavio;
Tauriello, Gerardo;
Bertoni, Martino;
Studer, Gabriel;
Smolinski, Anna;
Schwede, Torsten (2019).
Introducing "best single template" models as reference baseline for the Continuous Automated Model Evaluation (CAMEO). Proteins, 87 (12), 1378-1387.
Lepore, Rosalba;
Kryshtafovych, Andriy;
Alahuhta, Markus;
Veraszto, Harshul A.;
Bomble, Yannick J.;
Bufton, Joshua C.;
Bullock, Alex N.;
Caba, Cody;
Cao, Hongnan;
Davies, Owen R.;
Desfosses, Ambroise;
Dunne, Matthew;
Fidelis, Krzysztof;
Goulding, Celia W.;
Gurusaran, Manickam;
Gutsche, Irina;
Harding, Christopher J.;
Hartmann, Marcus D.;
Hayes, Christopher S.;
Joachimiak, Andrzej;
Leiman, Petr G.;
Loppnau, Peter;
Lovering, Andrew L.;
Lunin, Vladimir V.;
Michalska, Karolina;
Mir-Sanchis, Ignacio;
Mitra, Alok;
Moult, John;
Phillips, George N.;
Pinkas, Daniel M.;
Rice, Phoebe A.;
Tong, Yufeng;
Topf, Maya;
Walton, Jonathan D.;
Schwede, Torsten (2019).
Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins: Structure, Function, and Bioinformatics, 87 (12), 1037-1057.
Cheng, Jianlin;
Choe, Myong-Ho;
Elofsson, Arne;
Han, Kun-Sop;
Hou, Jie;
Maghrabi, Ali H. A.;
McGuffin, Liam J.;
Menéndez-Hurtado, David;
Olechnovič, Kliment;
Schwede, Torsten;
Studer, Gabriel;
Uziela, Karolis;
Venclovas, Česlovas;
Wallner, Björn (2019).
Estimation of model accuracy in CASP13. Proteins, 87 (12), 1361-1377.
Studer, Gabriel;
Tauriello, Gerardo;
Bienert, Stefan;
Waterhouse, Andrew Mark;
Bertoni, Martino;
Bordoli, Lorenza;
Schwede, Torsten;
Lepore, Rosalba (2019).
Modeling of Protein Tertiary and Quaternary Structures Based on Evolutionary Information. Methods in Molecular Biology, 1851, 301-316.
Studer, Gabriel;
Rempfer, Christine;
Waterhouse, Andrew M.;
Gumienny, Rafal;
Haas, Juergen;
Schwede, Torsten (2019).
QMEANDisCo - Distance Constraints Applied on Model Quality Estimation. Bioinformatics, 36 (6), 1765-1771.
2018
Waterhouse, Andrew;
Bertoni, Martino;
Bienert, Stefan;
Studer, Gabriel;
Tauriello, Gerardo;
Gumienny, Rafal;
Heer, Florian T.;
de Beer, Tjaart A. P.;
Rempfer, Christine;
Bordoli, Lorenza;
Lepore, Rosalba;
Schwede, Torsten (2018).
SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic acids research, 46 (W1), W296-W303.
Haas, Jürgen;
Barbato, Alessandro;
Behringer, Dario;
Studer, Gabriel;
Roth, Steven;
Bertoni, Martino;
Mostaguir, Khaled;
Gumienny, Rafal;
Schwede, Torsten (2018).
Continuous Automated Model Evaluation (CAMEO) Complementing the Critical Assessment of Structure Prediction in CASP12. Proteins, 86 Suppl 1, 387-398.
Kryshtafovych, Andriy;
Monastyrskyy, Bohdan;
Fidelis, Krzysztof;
Moult, John;
Schwede, Torsten;
Tramontano, Anna (2018).
Evaluation of the template-based modeling in CASP12. Proteins, 86 Suppl 1, 321-334.
Moult, John;
Fidelis, Krzysztof;
Kryshtafovych, Andriy;
Schwede, Torsten;
Tramontano, Anna (2018).
Critical assessment of methods of protein structure prediction (CASP) - Round XII. Proteins: Structure, Function, and Bioinformatics, 86 Suppl 1 (1), 7-15.
Lafita, Aleix;
Bliven, Spencer;
Kryshtafovych, Andriy;
Bertoni, Martino;
Monastyrskyy, Bohdan;
Duarte, Jose M.;
Schwede, Torsten;
Capitani, Guido (2018).
Assessment of protein assembly prediction in CASP12. Proteins: Structure, Function, and Bioinformatics, 86 Suppl 1 (1), 247-256.
Moult, John;
Fidelis, Krzysztof;
Kryshtafovych, Andriy;
Schwede, Torsten (2018).
A tribute to Anna Tramontano (1957-2017). Proteins: Structure, Function, and Bioinformatics, 86 (1), 5-6.
Kryshtafovych, Andriy;
Albrecht, Reinhard;
Baslé, Arnaud;
Bule, Pedro;
Caputo, Alessandro T.;
Carvalho, Ana Luisa;
Chao, Kinlin L.;
Diskin, Ron;
Fidelis, Krzysztof;
Fontes, Carlos M. G. A.;
Fredslund, Folmer;
Gilbert, Harry J.;
Goulding, Celia W.;
Hartmann, Marcus D.;
Hayes, Christopher S.;
Herzberg, Osnat;
Hill, Johan C.;
Joachimiak, Andrzej;
Kohring, Gert-Wieland;
Koning, Roman I.;
Lo Leggio, Leila;
Mangiagalli, Marco;
Michalska, Karolina;
Moult, John;
Najmudin, Shabir;
Nardini, Marco;
Nardone, Valentina;
Ndeh, Didier;
Nguyen, Thanh-Hong;
Pintacuda, Guido;
Postel, Sandra;
van Raaij, Mark J.;
Roversi, Pietro;
Shimon, Amir;
Singh, Abhimanyu K.;
Sundberg, Eric J.;
Tars, Kaspars;
Zitzmann, Nicole;
Schwede, Torsten (2018).
Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins: Structure, Function, and Bioinformatics, 86 Suppl 1 (1), 27-50.
2017
Glusman, Gustavo;
Rose, Peter W.;
Prlić, Andreas;
Dougherty, Jennifer;
Duarte, José M.;
Hoffman, Andrew S.;
Barton, Geoffrey J.;
Bendixen, Emøke;
Bergquist, Timothy;
Bock, Christian;
Brunk, Elizabeth;
Buljan, Marija;
Burley, Stephen K.;
Cai, Binghuang;
Carter, Hannah;
Gao, JianJiong;
Godzik, Adam;
Heuer, Michael;
Hicks, Michael;
Hrabe, Thomas;
Karchin, Rachel;
Leman, Julia Koehler;
Lane, Lydie;
Masica, David L.;
Mooney, Sean D.;
Moult, John;
Omenn, Gilbert S.;
Pearl, Frances;
Pejaver, Vikas;
Reynolds, Sheila M.;
Rokem, Ariel;
Schwede, Torsten;
Song, Sicheng;
Tilgner, Hagen;
Valasatava, Yana;
Zhang, Yang;
Deutsch, Eric W. (2017).
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome medicine, 9 (1), 113.
Burley, Stephen K.;
Kurisu, Genji;
Markley, John L.;
Nakamura, Haruki;
Velankar, Sameer;
Berman, Helen M.;
Sali, Andrej;
Schwede, Torsten;
Trewhella, Jill (2017).
PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models. Structure, 25 (9), 1317-1318.
Bertoni, Martino;
Kiefer, Florian;
Biasini, Marco;
Bordoli, Lorenza;
Schwede, Torsten (2017).
Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports, 7 (1), 10480.
Kryshtafovych, Andriy;
Monastyrskyy, Bohdan;
Fidelis, Krzysztof;
Schwede, Torsten;
Tramontano, Anna (2017).
Assessment of model accuracy estimations in CASP12. Proteins, 86 Suppl 1 (S1), 345-360.
Thornton, Janet M.;
Valencia, Alfonso;
Schwede, Torsten (2017).
Anna Tramontano 1957-2017. Nature Structural and Molecular Biology, 24 (5), 431-432.
Sprecher, Kathrin S.;
Hug, Isabelle;
Nesper, Jutta;
Potthoff, Eva;
Mahi, Mohamed-Ali;
Sangermani, Matteo;
Kaever, Volkhard;
Schwede, Torsten;
Vorholt, Julia;
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.
Romano, Valentina;
de Beer, Tjaart A. P.;
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), 104.
Bienert, Stefan;
Waterhouse, Andrew;
de Beer, Tjaart A. P.;
Tauriello, Gerardo;
Studer, Gabriel;
Bordoli, Lorenza;
Schwede, Torsten (2017).
The SWISS-MODEL Repository - new features and functionality. Nucleic Acids Research, 45 (D1), D313-D319.
Daina, Antoine;
Blatter, Marie-Claude;
Baillie Gerritsen, Vivienne;
Palagi, Patricia M.;
Marek, Diana;
Xenarios, Ioannis;
Schwede, Torsten;
Michielin, Olivier;
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), 335-344.
Heck, Angela;
Milnik, Annette;
Vukojevic, Vanja;
Petrovska, Jana;
Egli, Tobias;
Singer, Jochen;
Escobar, Pablo;
Sengstag, Thierry;
Coynel, David;
Freytag, Virginie;
Fastenrath, Matthias;
Demougin, Philippe;
Loos, Eva;
Hartmann, Francina;
Schicktanz, Nathalie;
Delarue Bizzini, Bernardo;
Vogler, Christian;
Kolassa, Iris-Tatjana;
Wilker, Sarah;
Elbert, Thomas;
Schwede, Torsten;
Beisel, Christian;
Beerenwinkel, Niko;
de Quervain, Dominique J.-F.;
Papassotiropoulos, Andreas (2017).
Exome sequencing of healthy phenotypic extremes links TROVE2 to emotional memory and PTSD. Nature Human Behaviour, 1 (4), 0081.
Trewhella, Jill;
Duff, Anthony P.;
Durand, Dominique;
Gabel, Frank;
Guss, J. Mitchell;
Hendrickson, Wayne A.;
Hura, Greg L.;
Jacques, David A.;
Kirby, Nigel M.;
Kwan, Ann H.;
P`erez, Javier;
Pollack, Lois;
Ryan, Timothy M.;
Sali, Andrej;
Schneidman-Duhovny, Dina;
Schwede, Torsten;
Svergun, Dmitri I.;
Sugiyama, Masaaki;
Tainer, John A.;
Vachette, Patrice;
Westbrook, John;
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 (Pt9), 710-728.
2016
Nicolet, Stefan;
Goldenberger, Daniel;
Schwede, Torsten;
Page, Malcolm;
Creus, Marc (2016).
Plasmid-mediated colistin resistance in a patient infected with Klebsiella pneumoniae. The Lancet Infectious Diseases, 16 (9), 998-999.
Dubey, Badri N.;
Lori, Christian;
Ozaki, Shogo;
Fucile, Geoffrey;
Plaza-Menacho, Ivan;
Jenal, Urs;
Schirmer, Tilman (2016).
Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking. Science Advances, 2 (9), e1600823.
Auffray, Charles;
Balling, Rudi;
Barroso, Inês;
Bencze, László;
Benson, Mikael;
Bergeron, Jay;
Bernal-Delgado, Enrique;
Blomberg, Niklas;
Bock, Christoph;
Conesa, Ana;
Del Signore, Susanna;
Delogne, Christophe;
Devilee, Peter;
Di Meglio, Alberto;
Eijkemans, Marinus;
Flicek, Paul;
Graf, Norbert;
Grimm, Vera;
Guchelaar, Henk-Jan;
Guo, Yi-Ke;
Gut, Ivo Glynne;
Hanbury, Allan;
Hanif, Shahid;
Hilgers, Ralf-Dieter;
Honrado, Ángel;
Hose, D Rod;
Houwing-Duistermaat, Jeanine;
Hubbard, Tim;
Janacek, Sophie Helen;
Karanikas, Haralampos;
Kievits, Tim;
Kohler, Manfred;
Kremer, Andreas;
Lanfear, Jerry;
Lengauer, Thomas;
Maes, Edith;
Meert, Theo;
Müller, Werner;
Nickel, Dörthe;
Oledzki, Peter;
Pedersen, Bertrand;
Petkovic, Milan;
Pliakos, Konstantinos;
Rattray, Magnus;
I Màs, Josep Redón;
Schneider, Reinhard;
Sengstag, Thierry;
Serra-Picamal, Xavier;
Spek, Wouter;
Vaas, Lea A I;
van Batenburg, Okker;
Vandelaer, Marc;
Varnai, Peter;
Villoslada, Pablo;
Vizcaíno, Juan Antonio;
Wubbe, John Peter Mary;
Zanetti, Gianluigi (2016).
Making sense of big data in health research: Towards an EU action plan. Genome medicine, 8 (1), 71.
Moult, John;
Fidelis, Krzysztof;
Kryshtafovych, Andriy;
Schwede, Torsten;
Tramontano, Anna (2016).
Critical assessment of methods of protein structure prediction: Progress and new directions in round XI. Proteins: Structure, Function, and Bioinformatics, 84 Suppl 1 (1), 4-14.
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.
Kryshtafovych, Andriy;
Moult, John;
Baslé, Arnaud;
Burgin, Alex;
Craig, Timothy K.;
Edwards, Robert A.;
Fass, Deborah;
Hartmann, Marcus D.;
Korycinski, Mateusz;
Lewis, Richard J.;
Lorimer, Donald;
Lupas, Andrei N.;
Newman, Janet;
Peat, Thomas S.;
Piepenbrink, Kurt H.;
Prahlad, Janani;
van Raaij, Mark J.;
Rohwer, Forest;
Segall, Anca M.;
Seguritan, Victor;
Sundberg, Eric J.;
Singh, Abhimanyu K.;
Wilson, Mark A.;
Schwede, Torsten (2016).
Some of the most interesting CASP11 targets through the eyes of their authors. Proteins: Structure, Function, and Bioinformatics, 84 (1), 34-50.
Kryshtafovych, Andriy;
Barbato, Alessandro;
Monastyrskyy, Bohdan;
Fidelis, Krzysztof;
Schwede, Torsten;
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, 84 (Suppl1), 349-69.
2015
Westbrook, John D. (2015).
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure: with folding and design, 23 (7), 1156-67.
Ihssen, Julian;
Haas, Jürgen;
Kowarik, Michael;
Wiesli, Luzia;
Wacker, Michael;
Schwede, Torsten;
Thöny-Meyer, Linda (2015).
Increased efficiency of Campylobacter jejuni N-oligosaccharyltransferase PglB by structure-guided engineering. Open biology, 5 (4), 140227.
Berman, Helen M;
Gabanyi, Margaret J;
Groom, Colin R;
Johnson, John E;
Murshudov, Garib N;
Nicholls, Robert A;
Reddy, Vijay;
Schwede, Torsten;
Zimmerman, Matthew D;
Westbrook, John;
Minor, Wladek (2015).
Data to knowledge: how to get meaning from your result. IUCrJ, 2 (Pt1), 45-58.
2014
Schmidt, Tobias B.;
Schwede, Torsten;
Meuwly, Markus (2014).
Computational Analysis of Methyl Transfer Reactions in Dengue Virus Methyltransferase. Journal of Physical Chemistry B, 118 (22), 5882-5890.
Stockinger, Heinz;
Altenhoff, Adrian M.;
Arnold, Konstantin;
Bairoch, Amos;
Bastian, Frederic;
Bergmann, Sven;
Bougueleret, Lydie;
Bucher, Philipp;
Delorenzi, Mauro;
Lane, Lydie;
Mercier, Philippe Le;
Lisacek, Frédérique;
Michielin, Olivier;
Palagi, Patricia M.;
Rougemont, Jacques;
Schwede, Torsten;
Mering, Christian von;
Nimwegen, Erik van;
Walther, Daniel;
Xenarios, Ioannis;
Zavolan, Mihaela;
Zdobnov, Evgeny M.;
Zoete, Vincent;
Appel, Ron D. (2014).
Fifteen years SIB Swiss Institute of Bioinformatics : life science databases, tools and support. Nucleic Acids Research, 42 (WebServerissue), W436-41.
Biasini, Marco;
Bienert, Stefan;
Waterhouse, Andrew;
Arnold, Konstantin;
Studer, Gabriel;
Schmidt, Tobias;
Kiefer, Florian;
Cassarino, Tiziano Gallo;
Bertoni, Martino;
Bordoli, Lorenza;
Schwede, Torsten (2014).
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42 (WebServerissue), W252-8.
Moult, John;
Fidelis, Krzysztof;
Kryshtafovych, Andriy;
Schwede, Torsten;
Tramontano, Anna (2014).
Critical assessment of methods of protein structure prediction (CASP) - round X. Proteins, 82 Suppl 2 (S2), 1-6.
Kryshtafovych, Andriy;
Moult, John;
Bales, Patrick;
Bazan, J. Fernando;
Biasini, Marco;
Burgin, Alex;
Chen, Chen;
Cochran, Frank V.;
Craig, Timothy K.;
Das, Rhiju;
Fass, Deborah;
Garcia-Doval, Carmela;
Herzberg, Osnat;
Lorimer, Donald;
Luecke, Hartmut;
Ma, Xiaolei;
Nelson, Daniel C.;
van Raaij, Mark J.;
Rohwer, Forest;
Segall, Anca;
Seguritan, Victor;
Zeth, Kornelius;
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, 82 (S2), 26-42.
Schmidt, Tobias;
Bergner, Andreas;
Schwede, Torsten (2014).
Modelling three-dimensional protein structures for applications in drug design. Drug discovery today, 19 (7), 890-7.
Kryshtafovych, Andriy;
Barbato, Alessandro;
Fidelis, Krzysztof;
Monastyrskyy, Bohdan;
Schwede, Torsten;
Tramontano, Anna (2014).
Assessment of the assessment : evaluation of the model quality estimates in CASP10. Proteins, 82 Suppl 2 (S2), 112-26.
Studer, Gabriel;
Biasini, Marco;
Schwede, Torsten (2014).
Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane). Bioinformatics, 30 (17), i505-11.
Haas, Jürgen;
Schwede, Torsten (2014).
Unabhängige Validierung von Methoden zur Proteinstrukturvorhersage. Biospektrum, 20 (2), 236-237.
Gallo Cassarino, Tiziano;
Bordoli, Lorenza;
Schwede, Torsten (2014).
Assessment of ligand binding site predictions in CASP10. Proteins, 82 Suppl 2 (S2), 154-63.
2013
Schwede, Torsten (2013).
Protein modeling: what happened to the "protein structure gap"?. Structure: with folding and design, 21 (9), 1531-1540.
Mariani, Valerio;
Biasini, Marco;
Barbato, Alessandro;
Schwede, Torsten (2013).
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics, 29 (21), 2722-8.
Biasini, M;
Schmidt, T;
Bienert, S;
Mariani, V;
Studer, G;
Haas, J;
Johner, N;
Schenk, A D;
Philippsen, A;
Schwede, T (2013).
OpenStructure : an integrated software framework for computational structural biology. Acta crystallographica. Section D, Biological crystallography, 69 (Pt5), 701-9.
Trewhella, Jill;
Hendrickson, Wayne A;
Kleywegt, Gerard J;
Sali, Andrej;
Sato, Mamoru;
Schwede, Torsten;
Svergun, Dmitri I;
Tainer, John A;
Westbrook, John;
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, 21 (6), 875-81.
Haas, Juergen;
Roth, Steven;
Arnold, Konstantin;
Kiefer, Florian;
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The Protein Model Portal: a comprehensive resource for protein structure and model information. Database, 2013, bat031.
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Homology Modeling of Protein Structures. , in:
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2012
Schwede, Torsten;
Iber, Dagmar (2012).
ECCB 2012 : The 11th European Conference on Computational Biology. Bioinformatics, 28 (18), i303-i305.
Barbato, Alessandro;
Benkert, Pascal;
Schwede, Torsten;
Tramontano, Anna;
Kosinski, Jan (2012).
Improving your target-template alignment with MODalign. Bioinformatics, 28 (7), 1038-9.
Bordoli, Lorenza;
Schwede, Torsten:
Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal, in:
Orry, Andrew JW;
Abagyan, Ruben(Ed.). (2012).
Homology Modeling: Methods and Protocols, New York, USA: Humana Press, Vol. 857, S.107-36.
2011
Kryshtafovych, Andriy;
Moult, John;
Bartual, Sergio G.;
Bazan, J. Fernando;
Berman, Helen;
Casteel, Darren E.;
Christodoulou, Evangelos;
Everett, John K.;
Hausmann, Jens;
Heidebrecht, Tatjana;
Hills, Tanya;
Hui, Raymond;
Hunt, John F.;
Seetharaman, Jayaraman;
Joachimiak, Andrzej;
Kennedy, Michael A.;
Kim, Choel;
Lingel, Andreas;
Michalska, Karolina;
Montelione, Gaetano T.;
Otero, José M.;
Perrakis, Anastassis;
Pizarro, Juan C.;
van Raaij, Mark J.;
Ramelot, Theresa A.;
Rousseau, Francois;
Tong, Liang;
Wernimont, Amy K.;
Young, Jasmine;
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 Suppl 10 (S10), 6-20.
Mariani, Valerio;
Kiefer, Florian;
Schmidt, Tobias;
Haas, Juergen;
Schwede, Torsten (2011).
Assessment of template based protein structure predictions in CASP9. Proteins, 79 Suppl 10 (S10), 37-58.
Kinch, Lisa N.;
Shi, Shuoyong;
Cheng, Hua;
Cong, Qian;
Pei, Jimin;
Mariani, Valerio;
Schwede, Torsten;
Grishin, Nick V. (2011).
CASP9 target classification. Proteins, 79 (s10), 21-36.
Schmidt, Tobias;
Haas, Jürgen;
Gallo Cassarino, Tiziano;
Schwede, Torsten (2011).
Assessment of ligand-binding residue predictions in CASP9. Proteins, 79 Suppl 10 (S10), 126-36.
Gabanyi, Margaret J;
Adams, Paul D;
Arnold, Konstantin;
Bordoli, Lorenza;
Carter, Lester G;
Flippen-Andersen, Judith;
Gifford, Lida;
Haas, Juergen;
Kouranov, Andrei;
McLaughlin, William A;
Micallef, David I;
Minor, Wladek;
Shah, Raship;
Schwede, Torsten;
Tao, Yi-Ping;
Westbrook, John D;
Zimmerman, Matthew;
Berman, Helen M (2011).
The Structural Biology Knowledgebase : a portal to protein structures, sequences, functions, and methods. Journal of structural and functional genomics, 12 (2), 45-54.
Baud, Olivia;
Etter, Sylvain;
Spreafico, Morena;
Bordoli, Lorenza;
Schwede, Torsten;
Vogel, Horst;
Pick, Horst (2011).
The Mouse Eugenol Odorant Receptor : Structural and Functional Plasticity of a Broadly Tuned Odorant Binding Pocket. Biochemistry, 50 (5), 843-53.
Benkert, Pascal;
Biasini, Marco;
Schwede, Torsten (2011).
Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 27 (3), 343-50.
2010
Biasini, M.;
Mariani, V.;
Haas, J.;
Scheuber, S.;
Schenk, AD.;
Schwede, T.;
Philippsen, A. (2010).
OpenStructure: a flexible software framework for computational structural biology. Bioinformatics, 26 (20), 2626-8.
Podvinec, Michael;
Lim, Siew Pheng;
Schmidt, Tobias;
Scarsi, Marco;
Wen, Daying;
Sonntag, Louis-Sebastian;
Sanschagrin, Paul;
Shenkin, Peter S;
Schwede, Torsten (2010).
Novel Inhibitors of Dengue Virus Methyltransferase : discovery by in vitro-driven virtual screening on a Desktop Computer Grid. Journal of Medicinal Chemistry, 53 (4), 1483-95.
Haas, J.;
Schwede, T. (2010).
Protein Homology Modelling - Providing Three-dimensional Models for Proteins where Experimental Data is Missing. ERCIM News, 82, 20-21.
2009
Pick, Horst;
Etter, Sylvain;
Baud, Olivia;
Schmauder, Ralf;
Bordoli, Lorenza;
Schwede, Torsten;
Vogel, Horst (2009).
Dual activities of odorants on olfactory and nuclear hormone receptors. Journal of biological chemistry, 284 (44), 30547-55.
Benkert, Pascal;
Tosatto, Silvio C E;
Schwede, Torsten (2009).
Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins, 77 Suppl 9 (S9), 173-80.
Benkert, P.;
Kunzli, M.;
Schwede, T. (2009).
QMEAN server for protein model quality estimation. Nucleic Acids Research, 37 (WebServerissue), W510-4.
Schwede, T.;
Peitsch, M. C.:
Protein Structure Modeling and Docking at the Swiss Institute of Bioinformatics, in:
Appel, RD;
Feytmans, E.(Ed.). (2009).
Bioinformatics. A Swiss Perspective, New Jersey: World Scientific, S.219-246.
Bordoli, Lorenza;
Kiefer, Florian;
Arnold, Konstantin;
Benkert, Pascal;
Battey, James;
Schwede, Torsten (2009).
Protein structure homology modelling using SWISS-MODEL Workspace. Nature Protocols, 4 (1), 1-13.
Berman, H. M.;
Westbrook, J. D.;
Gabanyi, M. J.;
Tao, W.;
Shah, R.;
Kouranov, A.;
Schwede, T.;
Arnold, K.;
Kiefer, F.;
Bordoli, L.;
Kopp, J.;
Podvinec, M.;
Adams, P. D.;
Carter, L. G.;
Minor, W.;
Nair, R.;
Baer, J. L. (2009).
The protein structure initiative structural genomics knowledgebase. Nucleic Acids Research, 37 (1Supplement), D365-D368.
Duerig, Anna;
Abel, Sören;
Folcher, Marc;
Nicollier, Micael;
Schwede, Torsten;
Amiot, Nicolas;
Giese, Bernd;
Jenal, Urs (2009).
Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression. Genes & development, 23 (1), 93-104.
Kiefer, F.;
Arnold, K.;
Kunzli, M.;
Bordoli, L.;
Schwede, T. (2009).
The Swiss-model Repository and associated resources. Nucleic Acids Research, 37 (1Supplement), D387-D392.
Schwede, Torsten;
Sali, Andrej;
Honig, Barry;
Levitt, Michael;
Berman, Helen M;
Jones, David;
Brenner, Steven E;
Burley, Stephen K;
Das, Rhiju;
Dokholyan, Nikolay V;
Dunbrack, Roland L;
Fidelis, Krzysztof;
Fiser, Andras;
Godzik, Adam;
Huang, Yuanpeng Janet;
Humblet, Christine;
Jacobson, Matthew P;
Joachimiak, Andrzej;
Krystek, Stanley R;
Kortemme, Tanja;
Kryshtafovych, Andriy;
Montelione, Gaetano T;
Moult, John;
Murray, Diana;
Sanchez, Roberto;
Sosnick, Tobin R;
Standley, Daron M;
Stouch, Terry;
Vajda, Sandor;
Vasquez, Max;
Westbrook, John D;
Wilson, Ian A (2009).
Outcome of a workshop on applications of protein models in biomedical research. Structure, 17 (2), 151-9.
Benkert, Pascal;
Schwede, Torsten;
Tosatto, Silvio Ce (2009).
QMEANclust : estimation of protein model quality by combining a composite scoring function with structural density information. BMC Structural Biology, 9 (1), 35.
Guex, Nicolas;
Peitsch, Manuel C;
Schwede, Torsten (2009).
Automated comparative protein structure modeling with Swiss-model and Swiss-PdbViewer : a historical perspective. Electrophoresis, 30 Suppl 1 (S1), S162-73.
Arnold, K.;
Kiefer, F.;
Kopp, J.;
Battey, J. N.;
Podvinec, M.;
Westbrook, J. D.;
Berman, H. M.;
Bordoli, L.;
Schwede, T. (2009).
The protein model portal. Journal of structural and functional genomics, 10 (1), 1-8.
2008
Schwede, T.;
Sali, A.;
Eswar, N.;
Peitsch, M. C.:
Protein Structure Modeling, in:
Schwede, T.;
Peitsch, M.C.(Ed.). (2008).
Computational structural biology, Singapore: World Scientific, S.700.
Podvinec, M.;
Schwede, T.;
Peitsch, M. C.:
Docking for neglected diseases as community efforts, in:
Schwede T,;
Peitsch MC,(Ed.). (2008).
Computational structural biology, Singapore: World Scientific Publishing, S.683-704.
2007
Zosso, D;
Podvinec, M;
Müller, M;
Aebersold, R;
Peitsch, M C;
Schwede, T (2007).
Tandem mass spectrometry protein identification on a PC grid. Studies in health technology and informatics, 126, 3-12.
Kopp, Jürgen;
Bordoli, Lorenza;
Battey, James N D;
Kiefer, Florian;
Schwede, Torsten (2007).
Assessment of CASP7 predictions for template-based modeling targets. Proteins, 69 Suppl 8, 38-56.
Bordoli, Lorenza;
Kiefer, Florian;
Schwede, Torsten (2007).
Assessment of disorder predictions in CASP7. Proteins, 69 Suppl 8, 129-36.
Battey, James N D;
Kopp, Jürgen;
Bordoli, Lorenza;
Read, Randy J;
Clarke, Neil D;
Schwede, Torsten (2007).
Automated server predictions in CASP7. Proteins, 69 Suppl 8, 68-82.
Michelsen, Kai;
Schmid, Volker;
Metz, Jutta;
Heusser, Katja;
Liebel, Urban;
Schwede, Torsten;
Spang, Anne;
Schwappach, Blanche (2007).
Novel cargo-binding site in the beta and delta subunits of coatomer. The Journal of cell biology, 179 (2), 209-17.
Clarke, Neil D;
Ezkurdia, Iakes;
Kopp, Jürgen;
Read, Randy J;
Schwede, Torsten;
Tress, Michael (2007).
Domain Definition and Target Classification for CASP7. Proteins, 69 Suppl 8 (S8), 10-8.
Scarsi, Marco;
Podvinec, Michael;
Roth, Adrian;
Hug, Hubert;
Kersten, Sander;
Albrecht, Hugo;
Schwede, Torsten;
Meyer, Urs A;
Rücker, Christoph (2007).
Sulfonylureas and glinides exhibit peroxisome proliferator-activated receptor gamma activity : a combined virtual screening and biological assay approach. Molecular pharmacology, 71 (2), 398-406.
Zosso, D.;
Arnold, K.;
Schwede, T.;
Podvinec, M.:
SWISS-TANDEM : a Web-based workspace for MS/MS protein identification on PC grid, in:
Kokol, P;
Podgorelec, V;
MiceticTurk, D;
Zorman, M;
Verlic, M(Ed.). (2007).
Twentieth IEEE international symposium on computer-based medical systems, Los Alamitos, Calif.: IEEE Computer Society, CBMS 2007.
Junne, Tina;
Schwede, Torsten;
Goder, Veit;
Spiess, Martin (2007).
Mutations in the Sec61p channel affecting signal sequence recognition and membrane protein topology. Journal of biological chemistry, 282 (45), 33201-9.
2006
Podvinec, M.;
Maffioletti, S.;
Kunszt, P.;
Arnold, K.;
Cerutti, L.;
Nyffeler, B.;
Schlapbach, R.;
Turker, C.;
Stockinger, H.;
Thomas, A. J.;
Peitsch, M. C.;
Schwede, T.:
The SwissBioGrid Project : objectives, preliminary results and lessons learnede-Science 2006 : 2nd IEEE International Conference on e-Science and Grid Computing, Los Alamitos, Calif.: IEEE Computer Society, e-Science 2006, 148.
Berman, Helen M;
Burley, Stephen K;
Chiu, Wah;
Sali, Andrej;
Adzhubei, Alexei;
Bourne, Philip E;
Bryant, Stephen H;
Dunbrack, Roland L;
Fidelis, Krzysztof;
Frank, Joachim;
Godzik, Adam;
Henrick, Kim;
Joachimiak, Andrzej;
Heymann, Bernard;
Jones, David;
Markley, John L;
Moult, John;
Montelione, Gaetano T;
Orengo, Christine;
Rossmann, Michael G;
Rost, Burkhard;
Saibil, Helen;
Schwede, Torsten;
Standley, Daron M;
Westbrook, John D (2006).
Outcome of a workshop on archiving structural models of biological macromolecules. Structure: with folding and design, 14 (8), 1211-7.
Kopp, J.;
Schwede, T. (2006).
The Swiss-model Repository : new features and functionalities. Nucleic Acids Research, 34 (D1), D315-D318.
Arnold, Konstantin;
Bordoli, Lorenza;
Kopp, Jürgen;
Schwede, Torsten (2006).
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics, 22 (2), 195-201.
Thorsteinsdottir, Holmfridur B.;
Schwede, Torsten;
Zoete, Vincent;
Meuwly, Markus (2006).
How inaccuracies in protein structure models affect estimates of protein-ligand interactions : computational analysis of HIV-I protease inhibitor binding. Proteins, 65 (2), 407-423.
Junne, T.;
Schwede, T.;
Goder, V.;
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), 4063-4068.
2004
Kopp, J.;
Schwede, T. (2004).
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. Nucleic Acids Research, 32 (1Supplement), D230-D234.
Kopp, Jurgen;
Schwede, Torsten (2004).
Automated protein structure homology modeling : a progress report. Pharmacogenomics, 5 (4), 405-16.
2003
Schwede, T.;
Kopp, J.;
Guex, N.;
Peitsch, M. C. (2003).
Swiss-model : an automated protein homology-modeling server. Nucleic Acids Research, 31 (13), 3381-5.
Fritzsche, Hanna B;
Schwede, Torsten;
Schulz, Georg E (2003).
Covalent and three-dimensional structure of the cyclodextrinase from Flavobacterium sp. no. 92. European journal of biochemistry, 270 (10), 2332-41.
Deutsch, Samuel;
Rideau, Alexandra;
Bochaton-Piallat, Marie-Luce;
Merla, Giuseppe;
Geinoz, Antoine;
Gabbiani, Giulio;
Schwede, Torsten;
Matthes, Thomas;
Antonarakis, Stylianos E.;
Beris, Photis (2003).
Asp1424Asn MYH9 mutation results in an unstable protein responsible for the phenotypes in May-Hegglin anomaly/Fechtner syndrome. Blood, 102 (2), 529-34.
2002
Kopp, J.;
Peitsch, M. C.;
Schwede, T.:
Protein Structure Modeling in Functional GenomicsFrontiers in Computational Genomics, Horizon Scientific Press: Horizon Scientific Press.
Peitsch, M.C.;
Schwede, T.;
Diemand, A.;
Guex, N. (2002).
Protein homology modeling. Nature encyclopedia of the human genome, 4.
Guex, Nicolas;
Schwede, Torsten;
Peitsch, Manuel C.:
Imaging science in biochemistry, in:
Hornak, Joseph P.(Ed.). (2002).
Encyclopedia of imaging science and technology, New York: John Wiley & Sons, n.a.(onlinebook).
Wattenhofer, M.;
Di Iorio, M.V.;
Rabionet, R.;
Dougherty, L.;
Pampanos, A.;
Schwede, T.;
Montserrat-Sentis, B.;
Arbones, M.L.;
Iliades, T.;
Pasquadibisceglie, A.;
D'Amelio, M.;
Alwan, S.;
Rossier, C.;
Dahl, H.H.M.;
Petersen, M.B.;
Estivill, X.;
Gasparini, P.;
Scott, H.S.;
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, 80, 124-131.
2001
Masmoudi, S;
Antonarakis, S E;
Schwede, T;
Ghorbel, A M;
Gratri, M;
Pappasavas, M P;
Drira, M;
Elgaied-Boulila, A;
Wattenhofer, M;
Rossier, C;
Scott, H S;
Ayadi, H;
Guipponi, M (2001).
Novel missense mutations of TMPRSS3 in two consanguineous Tunisian families with non-syndromic autosomal recessive deafness. Human mutation, 18 (2), 101-8.
2000
Peitsch, M C;
Schwede, T;
Guex, N (2000).
Automated protein modelling-the proteome in 3D. Pharmacogenomics, 1 (3), 257-66.
Schwede, T;
Diemand, A;
Guex, N;
Peitsch, M C (2000).
Protein structure computing in the genomic era. Research in microbiology, 151 (2), 107-12.
Guex, N.;
Schwede, T.;
Peitsch, M. C.:
Protein Tertiary Structure ModelingCurrent Protocols in Protein Science, [New York]: Wiley, nit 2.8.1-2.8.17, 2.8.1-2.8.17.
1999
Schwede, T. F.;
Retey, J.;
Schulz, G. E. (1999).
Crystal Structure of Histidine Ammonia-Lyase Revealing a Novel Polypeptide Modification as the Catalytic Electrophile. Biochemistry, 38 (17), 5355-61.
Schwede, T. F.;
Badeker, M.;
Langer, M.;
Retey, J.;
Schulz, G. E. (1999).
Homogenization and Crystallization of Histidine Ammonia-Lyase by Exchange of a Surface Cysteine Residue. Protein Engineering, 12 (2), 151-3.
