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

19 March 2023

Durairaj, Janani and Waterhouse, Andrew M. and Mets, Toomas and Brodiazhenko, Tetiana and Abdullah, Minhal and Studer, Gabriel and Akdel, Mehmet and Andreeva, Antonina and Bateman, Alex and Tenson, Tanel and Hauryliuk, Vasili and Schwede, Torsten and Pereira, Joana. (2023) What is hidden in the darkness? Deep-learning assisted large-scale protein family curation uncovers novel protein families and folds.

2023

Alexander, Leila T. and Durairaj, Janani and Kryshtafovych, Andriy and Abriata, Luciano A. and Bayo, Yusupha and Bhabha, Gira and Breyton, Cécile and Caulton, Simon G. and Chen, James and Degroux, Séraphine and Ekiert, Damian C. and Erlandsen, Benedikte S. and Freddolino, Peter L. and Gilzer, Dominic and Greening, Chris and Grimes, Jonathan M. and Grinter, Rhys and Gurusaran, Manickam and Hartmann, Marcus D. and Hitchman, Charlie J. and Keown, Jeremy R. and Kropp, Ashleigh and Kursula, Petri and Lovering, Andrew L. and Lemaitre, Bruno and Lia, Andrea and Liu, Shiheng and Logotheti, Maria and Lu, Shuze and Markússon, Sigurbjörn and Miller, Mitchell D. and Minasov, George and Niemann, Hartmut H. and Opazo, Felipe and Phillips, George N. and Davies, Owen R. and Rommelaere, Samuel and Rosas-Lemus, Monica and Roversi, Pietro and Satchell, Karla and Smith, Nathan and Wilson, Mark A. and Wu, Kuan-Lin and Xia, Xian and Xiao, Han and Zhang, Wenhua and Zhou, Z. Hong and Fidelis, Krzysztof and Topf, Maya and Moult, John and Schwede, Torsten. (2023) Protein target highlights in CASP15: Analysis of models by structure providers. Proteins: Structure, Function, and Bioinformatics . Online ahead of print..

Asllanaj, Erblin. Mapping the 3D Space of drug resistance variants. 2023, Doctoral Thesis, University of Basel, Faculty of Science.

Durairaj, Janani and Waterhouse, Andrew M. and Mets, Toomas and Brodiazhenko, Tetiana and Abdullah, Minhal and Studer, Gabriel and Tauriello, Gerardo and Akdel, Mehmet and Andreeva, Antonina and Bateman, Alex and Tenson, Tanel and Hauryliuk, Vasili and Schwede, Torsten and Pereira, Joana. (2023) Uncovering new families and folds in the natural protein universe. Nature, 622 (7983). pp. 646-653.

Kryshtafovych, Andriy and Antczak, Maciej and Szachniuk, Marta and Zok, Tomasz and Kretsch, Rachael C. and Rangan, Ramya and Pham, Phillip and Das, Rhiju and Robin, Xavier and Studer, Gabriel and Durairaj, Janani and Eberhardt, Jerome and Sweeney, Aaron and Topf, Maya and Schwede, Torsten and Fidelis, Krzysztof and Moult, John. (2023) New prediction categories in CASP15. Proteins: Structure, Function, and Bioinformatics .

Marone, Romina and Landmann, Emmanuelle and Devaux, Anna and Lepore, Rosalba and Seyres, Denis and Zuin, Jessica and Burgold, Thomas and Engdahl, Corinne and Capoferri, Giuseppina and Dell'Aglio, Alessandro and Larrue, Clément and Simonetta, Federico and Rositzka, Julia and Rhiel, Manuel and Andrieux, Geoffroy and Gallagher, Danielle N. and Schröder, Markus S. and Wiederkehr, Amélie and Sinopoli, Alessandro and Do Sacramento, Valentin and Haydn, Anna and Garcia-Prat, Laura and Divsalar, Christopher and Camus, Anna and Xu, Liwen and Bordoli, Lorenza and Schwede, Torsten and Porteus, Matthew and Tamburini, Jérôme and Corn, Jacob E. and Cathomen, Toni and Cornu, Tatjana I. and Urlinger, Stefanie and Jeker, Lukas T.. (2023) Epitope-engineered human hematopoietic stem cells are shielded from CD123-targeted immunotherapy. Journal of Experimental Medicine, 220 (12). e20231235ad of print.

Schweke, Hugo and Xu, Qifang and Tauriello, Gerardo and Pantolini, Lorenzo and Schwede, Torsten and Cazals, Frédéric and Lhéritier, Alix and Fernandez-Recio, Juan and Rodríguez-Lumbreras, Luis Angel and Schueler-Furman, Ora and Varga, Julia K. and Jiménez-García, Brian and Réau, Manon F. and Bonvin, Alexandre M. J. J. and Savojardo, Castrense and Martelli, Pier-Luigi and Casadio, Rita and Tubiana, Jérôme and Wolfson, Haim J. and Oliva, Romina and Barradas-Bautista, Didier and Ricciardelli, Tiziana and Cavallo, Luigi and Venclovas, Česlovas and Olechnovič, Kliment and Guerois, Raphael and Andreani, Jessica and Martin, Juliette and Wang, Xiao and Terashi, Genki and Sarkar, Daipayan and Christoffer, Charles and Aderinwale, Tunde and Verburgt, Jacob and Kihara, Daisuke and Marchand, Anthony and Correia, Bruno E. and Duan, Rui and Qiu, Liming and Xu, Xianjin and Zhang, Shuang and Zou, Xiaoqin and Dey, Sucharita and Dunbrack, Roland L. and Levy, Emmanuel D. and Wodak, Shoshana J.. (2023) Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study. Proteomics, 23 (17). e2200323.

Vallat, Brinda and Tauriello, Gerardo and Bienert, Stefan and Haas, Juergen and Webb, Benjamin M. and Zheng, Wei and Peisach, Ezra and Piehl, Dennis W. and Anischanka, Ivan and Sillitoe, Ian and Tolchard, James and Varadi, Mihaly and Baker, David and Orengo, Christine and Zhang, Yang and Hoch, Jeffrey C. and Kurisu, Genji and Patwardhan, Ardan and Velankar, Sameer and Burley, Stephen K. and Sali, Andrej and Schwede, Torsten and Berman, Helen M. and Westbrook, John D.. (2023) ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models. Journal of Molecular Biology, 435 (14). p. 168021.

20 December 2022

Pantolini, Lorenzo and Studer, Gabriel and Pereira, Joana and Durairaj, Janani and Schwede, Torsten . (2022) Embedding-based alignment: combining protein language models and alignment approaches to detect structural similarities in the twilight-zone.

13 October 2022

Durairaj, Janani and Pereira, Joana and Akdel, Mehmet and Schwede, Torsten. (2022) What is hidden in the darkness? Characterization of AlphaFold structural space.

9 October 2022

Topitsch, Annika and Schwede, Torsten and Pereira, Joana. (2022) Outer membrane β-barrel structure prediction through the lens of AlphaFold2.

2022

Akdel, Mehmet and Pires, Douglas E. V. and Pardo, Eduard Porta and Jänes, Jürgen and Zalevsky, Arthur O. and Mészáros, Bálint and Bryant, Patrick and Good, Lydia L. and Laskowski, Roman A. and Pozzati, Gabriele and Shenoy, Aditi and Zhu, Wensi and Kundrotas, Petras and Serra, Victoria Ruiz and Rodrigues, Carlos H. M. and Dunham, Alistair S. and Burke, David and Borkakoti, Neera and Velankar, Sameer and Frost, Adam and Basquin, Jérôme and Lindorff-Larsen, Kresten and Bateman, Alex and Kajava, Andrey V. and Valencia, Alfonso and Ovchinnikov, Sergey and Durairaj, Janani and Ascher, David B. and Thornton, Janet M. and Davey, Norman E. and Stein, Amelie and Elofsson, Arne and Croll, Tristan I. and Beltrao, Pedro. (2022) A structural biology community assessment of AlphaFold2 applications. Nature Structural and Molecular Biology, 29 (11). pp. 1056-1067.

Alt, Silke and Haggstrom, Douglas and Kessmann, Helmut and Kloss, Florian and Schneider, Christian Elias and Jäger, Timo and Schwede, Torsten and Brakhage, Axel and Dehio, Christoph. (2022) INCATE: a partnership to boost the antibiotic pipeline. Nature Reviews. Drug Discovery, 21 (9). pp. 621-622.

Varadi, Mihaly and Nair, Sreenath and Sillitoe, Ian and Tauriello, Gerardo and Anyango, Stephen and Bienert, Stefan and Borges, Clemente and Deshpande, Mandar and Green, Tim and Hassabis, Demis and Hatos, Andras and Hegedus, Tamas and Hekkelman, Maarten L. and Joosten, Robbie and Jumper, John and Laydon, Agata and Molodenskiy, Dmitry and Piovesan, Damiano and Salladini, Edoardo and Salzberg, Steven L. and Sommer, Markus J. and Steinegger, Martin and Suhajda, Erzsebet and Svergun, Dmitri and Tenorio-Ku, Luiggi and Tosatto, Silvio and Tunyasuvunakool, Kathryn and Waterhouse, Andrew Mark and Schwede, Torsten and Orengo, Christine and Velankar, Sameer. (2022) 3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources. GigaScience, 11. giac118.

2021

Alexander, Leila T. and Lepore, Rosalba and Kryshtafovych, Andriy and Adamopoulos, Athanassios and Alahuhta, Markus and Arvin, Ann M. and Bomble, Yannick J. and Böttcher, Bettina and Breyton, Cécile and Chiarini, Valerio and Chinnam, Naga Babu and Chiu, Wah and Fidelis, Krzysztof and Grinter, Rhys and Gupta, Gagan D. and Hartmann, Marcus D. and Hayes, Christopher S. and Heidebrecht, Tatjana and Ilari, Andrea and Joachimiak, Andrzej and Kim, Youngchang and Linares, Romain and Lovering, Andrew L. and Lunin, Vladimir V. and Lupas, Andrei N. and Makbul, Cihan and Michalska, Karolina and Moult, John and Mukherjee, Prasun K. and Nutt, William Sam and Oliver, Stefan L. and Perrakis, Anastassis and Stols, Lucy and Tainer, John A. and Topf, Maya and Tsutakawa, Susan E. and Valdivia-Delgado, Mauricio and Schwede, Torsten. (2021) Target highlights in CASP14: analysis of models by structure providers. Proteins: Structure, Function, and Bioinformatics . pp. 1-26.

Kryshtafovych, Andriy and Moult, John and Billings, Wendy M. and Della Corte, Dennis and Fidelis, Krzysztof and Kwon, Sohee and Olechnovič, Kliment and Seok, Chaok and Venclovas, Česlovas and Won, Jonghun and Casp-Covid participants, . (2021) Modeling SARS-CoV-2 proteins in the CASP-commons experiment. Proteins: Structure, Function, and Bioinformatics . pp. 1-10.

Kryshtafovych, Andriy and Schwede, Torsten and Topf, Maya and Fidelis, Krzysztof and Moult, John. (2021) Critical assessment of methods of protein structure prediction (CASP)-Round XIV. Proteins: Structure, Function, and Bioinformatics , 89 (12). pp. 1607-1617.

Mari, Alfredo and Roloff, Tim and Stange, Madlen and Søgaard, Kirstine K. and Asllanaj, Erblin and Tauriello, Gerardo and Alexander, Leila Tamara and Schweitzer, Michael and Leuzinger, Karoline and Gensch, Alexander and Martinez, Aurélien E. and Bielicki, Julia and Pargger, Hans and Siegemund, Martin and Nickel, Christian H. and Bingisser, Roland and Osthoff, Michael and Bassetti, Stefano and Sendi, Parham and Battegay, Manuel and Marzolini, Catia and Seth-Smith, Helena M. B. and Schwede, Torsten and Hirsch, Hans H. and Egli, Adrian. (2021) Global Genomic Analysis of SARS-CoV-2 RNA Dependent RNA Polymerase Evolution and Antiviral Drug Resistance. Microorganisms, 9 (5). p. 1094.

Pereira, Joana and Schwede, Torsten. (2021) Interactomes in the era of deep learning. Science, 374 (6573). pp. 1319-1320.

Rehm, Heidi L. and Page, Angela J. H. and Smith, Lindsay and Adams, Jeremy B. and Alterovitz, Gil and Babb, Lawrence J. and Barkley, Maxmillian P. and Baudis, Michael and Beauvais, Michael J. S. and Beck, Tim and Beckmann, Jacques S. and Beltran, Sergi and Bernick, David and Bernier, Alexander and Bonfield, James K. and Boughtwood, Tiffany F. and Bourque, Guillaume and Bowers, Sarion R. and Brookes, Anthony J. and Brudno, Michael and Brush, Matthew H. and Bujold, David and Burdett, Tony and Buske, Orion J. and Cabili, Moran N. and Cameron, Daniel L. and Carroll, Robert J. and Casas-Silva, Esmeralda and Chakravarty, Debyani and Chaudhari, Bimal P. and Chen, Shu Hui and Cherry, J. Michael and Chung, Justina and Cline, Melissa and Clissold, Hayley L. and Cook-Deegan, Robert M. and Courtot, Mélanie and Cunningham, Fiona and Cupak, Miro and Davies, Robert M. and Denisko, Danielle and Doerr, Megan J. and Dolman, Lena I. and Dove, Edward S. and Dursi, L. Jonathan and Dyke, Stephanie O. M. and Eddy, James A. and Eilbeck, Karen and Ellrott, Kyle P. and Fairley, Susan and Fakhro, Khalid A. and Firth, Helen V. and Fitzsimons, Michael S. and Fiume, Marc and Flicek, Paul and Fore, Ian M. and Freeberg, Mallory A. and Freimuth, Robert R. and Fromont, Lauren A. and Fuerth, Jonathan and Gaff, Clara L. and Gan, Weiniu and Ghanaim, Elena M. and Glazer, David and Green, Robert C. and Griffith, Malachi and Griffith, Obi L. and Grossman, Robert L. and Groza, Tudor and Guidry Auvil, Jaime M. and Guigó, Roderic and Gupta, Dipayan and Haendel, Melissa A. and Hamosh, Ada and Hansen, David P. and Hart, Reece K. and Hartley, Dean Mitchell and Haussler, David and Hendricks-Sturrup, Rachele M. and Ho, Calvin W. L. and Hobb, Ashley E. and Hoffman, Michael M. and Hofmann, Oliver M. and Holub, Petr and Hsu, Jacob Shujui and Hubaux, Jean-Pierre and Hunt, Sarah E. and Husami, Ammar and Jacobsen, Julius O. and Jamuar, Saumya S. and Janes, Elizabeth L. and Jeanson, Francis and Jené, Aina and Johns, Amber L. and Joly, Yann and Jones, Steven J. M. and Kanitz, Alexander and Kato, Kazuto and Keane, Thomas M. and Kekesi-Lafrance, Kristina and Kelleher, Jerome and Kerry, Giselle and Khor, Seik-Soon and Knoppers, Bartha M. and Konopko, Melissa A. and Kosaki, Kenjiro and Kuba, Martin and Lawson, Jonathan and Leinonen, Rasko and Li, Stephanie and Lin, Michael F. and Linden, Mikael and Liu, Xianglin and Liyanage, Isuru Udara and Lopez, Javier and Lucassen, Anneke M. and Lukowski, Michael and Mann, Alice L. and Marshall, John and Mattioni, Michele and Metke-Jimenez, Alejandro and Middleton, Anna and Milne, Richard J. and Molnár-Gábor, Fruzsina and Mulder, Nicola and Munoz-Torres, Monica C. and Nag, Rishi and Nakagawa, Hidewaki and Nasir, Jamal and Navarro, Arcadi and Nelson, Tristan H. and Niewielska, Ania and Nisselle, Amy and Niu, Jeffrey and Nyrönen, Tommi H. and O'Connor, Brian D. and Oesterle, Sabine and Ogishima, Soichi and Wang, Vivian Ota and Paglione, Laura A. D. and Palumbo, Emilio and Parkinson, Helen E. and Philippakis, Anthony A. and Pizarro, Angel D. and Prlic, Andreas and Rambla, Jordi and Rendon, Augusto and Rider, Renee A. and Robinson, Peter N. and Rodarmer, Kurt W. and Rodriguez, Laura Lyman and Rubin, Alan F. and Rueda, Manuel and Rushton, Gregory A. and Ryan, Rosalyn S. and Saunders, Gary I. and Schuilenburg, Helen and Schwede, Torsten and Scollen, Serena and Senf, Alexander and Sheffield, Nathan C. and Skantharajah, Neerjah and Smith, Albert V. and Sofia, Heidi J. and Spalding, Dylan and Spurdle, Amanda B. and Stark, Zornitza and Stein, Lincoln D. and Suematsu, Makoto and Tan, Patrick and Tedds, Jonathan A. and Thomson, Alastair A. and Thorogood, Adrian and Tickle, Timothy L. and Tokunaga, Katsushi and Törnroos, Juha and Torrents, David and Upchurch, Sean and Valencia, Alfonso and Guimera, Roman Valls and Vamathevan, Jessica and Varma, Susheel and Vears, Danya F. and Viner, Coby and Voisin, Craig and Wagner, Alex H. and Wallace, Susan E. and Walsh, Brian P. and Williams, Marc S. and Winkler, Eva C. and Wold, Barbara J. and Wood, Grant M. and Woolley, J. Patrick and Yamasaki, Chisato and Yates, Andrew D. and Yung, Christina K. and Zass, Lyndon J. and Zaytseva, Ksenia and Zhang, Junjun and Goodhand, Peter and North, Kathryn and Birney, Ewan. (2021) GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genomics, 1 (2). p. 100029.

Robin, Xavier and Haas, Juergen and Gumienny, Rafal and Smolinski, Anna and Tauriello, Gerardo and Schwede, Torsten. (2021) Continuous Automated Model Evaluation (CAMEO)-Perspectives on the future of fully automated evaluation of structure prediction methods. Proteins: Structure, Function, and Bioinformatics , 89 (12). pp. 1977-1986.

Studer, Gabriel and Tauriello, Gerardo and Bienert, Stefan and Biasini, Marco and Johner, Niklaus and Schwede, Torsten. (2021) ProMod3-A versatile homology modelling toolbox. PLoS Computational Biology, 17 (1). e1008667.

2020

Bignucolo, Olivier and Bernèche, Simon. (2020) The Voltage-Dependent Deactivation of the KvAP Channel Involves the Breakage of Its S4 Helix. Frontiers in molecular biosciences, 7. p. 162.

Coman Schmid, Diana and Crameri, Katrin and Oesterle, Sabine and Rinn, Bernd and Sengstag, Thierry and Stockinger, Heinz and 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. pp. 1170-1174.

Gervasoni, Silvia and Vistoli, Giulio and Talarico, Carmine and Manelfi, Candida and Beccari, Andrea R. and Studer, Gabriel and Tauriello, Gerardo and Waterhouse, Andrew Mark and Schwede, Torsten and 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). p. 5152.

Righetto, Ricardo D. and Anton, Leonie and Adaixo, Ricardo and Jakob, Roman P. and Zivanov, Jasenko and Mahi, Mohamed-Ali and Ringler, Philippe and Schwede, Torsten and Maier, Timm and Stahlberg, Henning. (2020) Author Correction: High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica. Nature Communications, 11 (1). p. 5873.

Righetto, Ricardo D. and Anton, Leonie and Adaixo, Ricardo and Jakob, Roman P. and Zivanov, Jasenko and Mahi, Mohamed-Ali and Ringler, Philippe and Schwede, Torsten and Maier, Timm and Stahlberg, Henning. (2020) High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica. Nature Communications, 11 (1). p. 5101.

2019

Berman, Helen M. and Adams, Paul D. and Bonvin, Alexandre A. and Burley, Stephen K. and Carragher, Bridget and Chiu, Wah and DiMaio, Frank and Ferrin, Thomas E. and Gabanyi, Margaret J. and Goddard, Thomas D. and Griffin, Patrick R. and Haas, Juergen and Hanke, Christian A. and Hoch, Jeffrey C. and Hummer, Gerhard and Kurisu, Genji and Lawson, Catherine L. and Leitner, Alexander and Markley, John L. and Meiler, Jens and Montelione, Gaetano T. and Phillips, George N. and Prisner, Thomas and Rappsilber, Juri and Schriemer, David C. and Schwede, Torsten and Seidel, Claus A. M. and Strutzenberg, Timothy S. and Svergun, Dmitri I. and Tajkhorshid, Emad and Trewhella, Jill and Vallat, Brinda and Velankar, Sameer and Vuister, Geerten W. and Webb, Benjamin and Westbrook, John D. and White, Kate L. and Sali, Andrej. (2019) Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure (London, England : 1993), 27 (12). pp. 1745-1759.

Cheng, Jianlin and Choe, Myong-Ho and Elofsson, Arne and Han, Kun-Sop and Hou, Jie and Maghrabi, Ali H. A. and McGuffin, Liam J. and Menéndez-Hurtado, David and Olechnovič, Kliment and Schwede, Torsten and Studer, Gabriel and Uziela, Karolis and Venclovas, Česlovas and Wallner, Björn. (2019) Estimation of model accuracy in CASP13. Proteins, 87 (12). pp. 1361-1377.

Haas, Juergen and Gumienny, Rafal and Barbato, Alessandro and Ackermann, Flavio and Tauriello, Gerardo and Bertoni, Martino and Studer, Gabriel and Smolinski, Anna and Schwede, Torsten. (2019) Introducing "best single template" models as reference baseline for the Continuous Automated Model Evaluation (CAMEO). Proteins, 87 (12). pp. 1378-1387.

Krause, Arthur. Deciphering the clonal evolution of non-small cell lung cancer. 2019, Doctoral Thesis, University of Basel, Faculty of Science.

Kryshtafovych, Andriy and Schwede, Torsten and Topf, Maya and Fidelis, Krzysztof and Moult, John. (2019) Critical assessment of methods of protein structure prediction (CASP)-Round XIII. Proteins, 87 (12). pp. 1011-1020.

Lepore, Rosalba and Kryshtafovych, Andriy and Alahuhta, Markus and Veraszto, Harshul A. and Bomble, Yannick J. and Bufton, Joshua C. and Bullock, Alex N. and Caba, Cody and Cao, Hongnan and Davies, Owen R. and Desfosses, Ambroise and Dunne, Matthew and Fidelis, Krzysztof and Goulding, Celia W. and Gurusaran, Manickam and Gutsche, Irina and Harding, Christopher J. and Hartmann, Marcus D. and Hayes, Christopher S. and Joachimiak, Andrzej and Leiman, Petr G. and Loppnau, Peter and Lovering, Andrew L. and Lunin, Vladimir V. and Michalska, Karolina and Mir-Sanchis, Ignacio and Mitra, Alok and Moult, John and Phillips, George N. and Pinkas, Daniel M. and Rice, Phoebe A. and Tong, Yufeng and Topf, Maya and Walton, Jonathan D. and Schwede, Torsten. (2019) Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins: Structure, Function, and Bioinformatics , 87 (12). pp. 1037-1057.

Studer, Gabriel and Rempfer, Christine and Waterhouse, Andrew M. and Gumienny, Rafal and Haas, Juergen and Schwede, Torsten. (2019) QMEANDisCo - Distance Constraints Applied on Model Quality Estimation. Bioinformatics, 36 (6). pp. 1765-1771.

Studer, Gabriel and Tauriello, Gerardo and Bienert, Stefan and Waterhouse, Andrew Mark and Bertoni, Martino and Bordoli, Lorenza and Schwede, Torsten and Lepore, Rosalba. (2019) Modeling of Protein Tertiary and Quaternary Structures Based on Evolutionary Information. Methods in Molecular Biology, 1851. pp. 301-316.

2018

Haas, Jürgen and Barbato, Alessandro and Behringer, Dario and Studer, Gabriel and Roth, Steven and Bertoni, Martino and Mostaguir, Khaled and Gumienny, Rafal and Schwede, Torsten. (2018) Continuous Automated Model Evaluation (CAMEO) Complementing the Critical Assessment of Structure Prediction in CASP12. Proteins, 86 Suppl 1. pp. 387-398.

Kryshtafovych, Andriy and Albrecht, Reinhard and Baslé, Arnaud and Bule, Pedro and Caputo, Alessandro T. and Carvalho, Ana Luisa and Chao, Kinlin L. and Diskin, Ron and Fidelis, Krzysztof and Fontes, Carlos M. G. A. and Fredslund, Folmer and Gilbert, Harry J. and Goulding, Celia W. and Hartmann, Marcus D. and Hayes, Christopher S. and Herzberg, Osnat and Hill, Johan C. and Joachimiak, Andrzej and Kohring, Gert-Wieland and Koning, Roman I. and Lo Leggio, Leila and Mangiagalli, Marco and Michalska, Karolina and Moult, John and Najmudin, Shabir and Nardini, Marco and Nardone, Valentina and Ndeh, Didier and Nguyen, Thanh-Hong and Pintacuda, Guido and Postel, Sandra and van Raaij, Mark J. and Roversi, Pietro and Shimon, Amir and Singh, Abhimanyu K. and Sundberg, Eric J. and Tars, Kaspars and Zitzmann, Nicole and Schwede, Torsten. (2018) Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins: Structure, Function, and Bioinformatics , 86 (1). pp. 27-50.

Kryshtafovych, Andriy and Monastyrskyy, Bohdan and Fidelis, Krzysztof and Moult, John and Schwede, Torsten and Tramontano, Anna. (2018) Evaluation of the template-based modeling in CASP12. Proteins, 86 Suppl 1. pp. 321-334.

Lafita, Aleix and Bliven, Spencer and Kryshtafovych, Andriy and Bertoni, Martino and Monastyrskyy, Bohdan and Duarte, Jose M. and Schwede, Torsten and Capitani, Guido. (2018) Assessment of protein assembly prediction in CASP12. Proteins: Structure, Function, and Bioinformatics , 86 (1). pp. 247-256.

Moult, John and Fidelis, Krzysztof and Kryshtafovych, Andriy and Schwede, Torsten. (2018) A tribute to Anna Tramontano (1957-2017). Proteins: Structure, Function, and Bioinformatics , 86 (1). pp. 5-6.

Moult, John and Fidelis, Krzysztof and Kryshtafovych, Andriy and Schwede, Torsten and Tramontano, Anna. (2018) Critical assessment of methods of protein structure prediction (CASP) - Round XII. Proteins: Structure, Function, and Bioinformatics , 86 (1). pp. 7-15.

Waterhouse, Andrew and Bertoni, Martino and Bienert, Stefan and Studer, Gabriel and Tauriello, Gerardo and Gumienny, Rafal and Heer, Florian T. and de Beer, Tjaart A. P. and Rempfer, Christine and Bordoli, Lorenza and Lepore, Rosalba and Schwede, Torsten. (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic acids research, 46 (W1). W296-W303.

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.

Glusman, Gustavo and Rose, Peter W. and Prlić, Andreas and Dougherty, Jennifer and Duarte, José M. and Hoffman, Andrew S. and Barton, Geoffrey J. and Bendixen, Emøke and Bergquist, Timothy and Bock, Christian and Brunk, Elizabeth and Buljan, Marija and Burley, Stephen K. and Cai, Binghuang and Carter, Hannah and Gao, JianJiong and Godzik, Adam and Heuer, Michael and Hicks, Michael and Hrabe, Thomas and Karchin, Rachel and Leman, Julia Koehler and Lane, Lydie and Masica, David L. and Mooney, Sean D. and Moult, John and Omenn, Gilbert S. and Pearl, Frances and Pejaver, Vikas and Reynolds, Sheila M. and Rokem, Ariel and Schwede, Torsten and Song, Sicheng and Tilgner, Hagen and Valasatava, Yana and Zhang, Yang and Deutsch, Eric W.. (2017) Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome medicine, 9 (1). p. 113.

Heer, Florian T. and Posson, David J. and Wojtas-Niziurski, Wojciech and Nimigean, Crina M. and Bernèche, Simon. (2017) Mechanism of activation at the selectivity filter of the KcsA K(+) channel. eLife, 6. e25844.

Johner, Niklaus B. and Berneche, Simon. (2017) Effect of Membrane Composition on Ion Conduction in a Voltage-Gated Potassium Channel. Biophysical Journal, 112 (3, Supplement 1). 542A.

Kryshtafovych, Andriy and Monastyrskyy, Bohdan and Fidelis, Krzysztof and Schwede, Torsten and Tramontano, Anna. (2017) Assessment of model accuracy estimations in CASP12. Proteins, 86 (S1). pp. 345-360.

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.

Studer, Gabriel. Efficient algorithms in protein modelling. 2017, Doctoral Thesis, University of Basel, Faculty of Science.

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.

Xu, Yanyan and Vien, Malvin and Liang, Chungwen and Accardi, Alessio and Berneche, Simon. (2017) Molecular Mechanism of Cl-/H+ Coupling in a CLC Antiporter. Biophysical Journal, 112 (3, Supplement 1). 336A.

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 (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.

Dubey, Badri N. and Lori, Christian and Ozaki, Shogo and Fucile, Geoffrey and Plaza-Menacho, Ivan and Jenal, Urs and Schirmer, Tilman. (2016) Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking. Science Advances, 2 (9). e1600823.

Heer, Florian. Molecular mechanics investigation of conductance regulation in selective K+ ion channels. 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.

Nicolet, Stefan and Goldenberger, Daniel and Schwede, Torsten and Page, Malcolm and Creus, Marc. (2016) Plasmid-mediated colistin resistance in a patient infected with Klebsiella pneumoniae. The Lancet Infectious Diseases, 16 (9). pp. 998-999.

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, 6 (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) OpenStructure: a flexible software framework for computational structural biology. Bioinformatics, 26 (20). 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, Jürgen and Schwede, Torsten. (2006) The Swiss-model Repository : new features and functionalities. Nucleic Acids Research, 34 (Suppl 1). 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, Samuel and Rideau, Alexandra and Bochaton-Piallat, Marie-Luce and Merla, Giuseppe and Geinoz, Antoine and Gabbiani, Giulio and Schwede, Torsten and Matthes, Thomas and Antonarakis, Stylianos E. and Beris, Photis. (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.