Prof. Dr. Torsten Schwede

Dörig, Christian, Marulli, Cathy, Peskett, Thomas, Volkmar, Norbert, Pantolini, Lorenzo, Studer, Gabriel, Paleari, Camilla, Frommelt, Fabian, Schwede, Torsten, de Souza, Natalie, Barral, Yves, & Picotti, Paola. (2025). Global profiling of protein complex dynamics with an experimental library of protein interaction markers. Nature Biotechnology, 43(5), 985–1001. https://doi.org/10.1038/s41587-024-02432-8

Krummenacher, Reto, Simsek, Osman Seckin, Leemann, Michèle, Alexander, Leila T., Schwede, Torsten, Ciorba, Florina M., & Pereira, Joana. (2025). Scalable Genomic Context Analysis with GCsnap2 on HPC Clusters [Proceedings-article]. Proceedings of the Platform for Advanced Scientific Computing Conference , 1–12. https://doi.org/10.1145/3732775.3733579

Pereira, Joana, Pantolini, Lorenzo, Durairaj, Janani, & Schwede, Torsten. (2025). Large-scale protein clustering in the age of deep learning [Journal-article]. Current Opinion in Structural Biology, 94. https://doi.org/10.1016/j.sbi.2025.103078

Marone, Romina, Asllanaj, Erblin, Capoferri, Giuseppina, Schwede, Torsten, Jeker, Lukas T, & Lepore, Rosalba. (2025). Impact of Human Genetic Variation Underlying Resistance to Antigen-Specific Immunotherapy [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.05.02.651174

Robin, Xavier, Škrinjar, Peter, Waterhouse, Andrew, Studer, Gabriel, Tauriello, Gerardo, Durairaj, Janani, & Schwede, Torsten. (2025). Benchmarking of macromolecular complexes with the Continuous Automated Model Evaluation (CAMEO) [Posted-content]. In Authorea. Authorea. https://doi.org/10.22541/au.174638718.83117953/v1

Molodenskiy, Dmitry, Maurer, Valentin J., Yu, Dingquan, Chojnowski, Grzegorz, Bienert, Stefan, Tauriello, Gerardo, Gilep, Konstantin, Schwede, Torsten, & Kosinski, Jan. (2025). AlphaPulldown2 - a general pipeline for high-throughput structural modeling. Bioinformatics, 41(3). https://doi.org/10.1093/bioinformatics/btaf115

Schwede, Torsten, Studer, Gabriel, Robin, Xavier, Bienert, Stefan, Durairaj, Janani, & Tauriello, Gerardo. (2025). Comparing macromolecular complexes - a fully automated benchmarking suite [Posted-content]. In Research Square. Springer Science and Business Media LLC. https://doi.org/10.21203/rs.3.rs-5920881/v1

Škrinjar, Peter, Eberhardt, Jérôme, Durairaj, Janani, & Schwede, Torsten. (2025). Have protein-ligand co-folding methods moved beyond memorisation? [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2025.02.03.636309

Vallat, Brinda, Webb, Benjamin M., Westbrook, John D., Goddard, Thomas D., Hanke, Christian A., Graziadei, Andrea, Peisach, Ezra, Zalevsky, Arthur, Sagendorf, Jared, Tangmunarunkit, Hongsuda, Voinea, Serban, Sekharan, Monica, Yu, Jian, Bonvin, Alexander A.M.J.J., DiMaio, Frank, Hummer, Gerhard, Meiler, Jens, Tajkhorshid, Emad, Ferrin, Thomas E., et al. (2024). IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. Journal of Molecular Biology, 436(17). https://doi.org/10.1016/j.jmb.2024.168546

Durairaj, Janani, Adeshina, Yusuf, Cao, Zhonglin, Zhang, Xuejin, Oleinikovas, Vladas, Duignan, Thomas, McClure, Zachary, Robin, Xavier, Studer, Gabriel, Kovtun, Daniel, Rossi, Emanuele, Zhou, Guoqing, Veccham, Srimukh, Isert, Clemens, Peng, Yuxing, Sundareson, Prabindh, Akdel, Mehmet, Corso, Gabriele, Stärk, Hannes, et al. (2024). PLINDER: The protein-ligand interactions dataset and evaluation resource [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2024.07.17.603955

Waterhouse, Andrew, Studer,Gabriel, Robin,Xavier, Bienert,Stefan, Tauriello,Gerardo, & Schwede,Torsten. (2024). The structure assessment web server: For proteins, complexes and more. Nucleic Acids Research, 52(W1), W318–W323. https://doi.org/10.1093/nar/gkae270

Palermo, G., Accordi, G., Gadioli, D., Zhang, Y., Vitali, E., Guindani, B., Ardagna, D., Silvano, C., Beccari, A. R., Bonanni, D., Talarico, C., Lughini, F., Biswas, A. D., Martinovic, J., Golasowski, M., Silva, P., Bohm, A., Beranek, J., Krenek, J., et al. (2024). LIGATE - LIgand Generator and portable drug discovery platform AT Exascale [Proceedings-article]. 20th ACM International Conference on Computing Frontiers, 2, 107–109. https://doi.org/10.1145/3637543.3656335

Durairaj, Janani, Follonier, Océane M., Leuzinger, Karoline, Alexander, Leila T., Wilhelm, Maud, Pereira, Joana, Hillenbrand, Caroline A., Weissbach, Fabian H, Schwede, Torsten, Hirsch, Hans H., & Greber, Urs F. (2024). Structural implications of BK polyomavirus sequence variations in the major viral capsid protein Vp1 and large T-antigen: a computational study. mSphere, 9(4), Online ahead of print. https://doi.org/10.1128/msphere.00799-23

Eberhardt, Jérôme, Lees, Aidan, Lill, Markus, & Schwede, Torsten. (2024). Combining Bayesian optimization with sequence- or structure-based strategies for optimization of peptide-binding protein [Posted-content]. In ChemRxiv. American Chemical Society (ACS). https://doi.org/10.26434/chemrxiv-2023-b7l81-v2

Pantolini, Lorenzo, Studer, Gabriel, Pereira, Joana, Durairaj, Janani, Tauriello, Gerardo, & Schwede, Torsten. (2024). Embedding-based alignment: combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone [Journal-article]. Bioinformatics, 40(1). https://doi.org/10.1093/bioinformatics/btad786

Topitsch, Annika, Schwede, Torsten, & Pereira, Joana. (2024). Outer membrane β-barrel structure prediction through the lens of AlphaFold2. Proteins: Structure, Function and Bioinformatics, 92(1), 3–14. https://doi.org/10.1002/prot.26552

Leemann, Michèle, Sagasta, Ander, Eberhardt, Jerome, Schwede, Torsten, Robin, Xavier, & Durairaj, Janani. (2023). Automated benchmarking of combined protein structure and ligand conformation prediction. Proteins: Structure, Function and Bioinformatics, 91(12), 1912–1924. https://doi.org/10.1002/prot.26605

Robin, Xavier, Studer, Gabriel, Durairaj, Janani, Eberhardt, Jerome, Schwede, Torsten, & Walters, W. Patrick. (2023). Assessment of protein–ligand complexes in CASP15. Proteins: Structure, Function and Bioinformatics, 91(12), 1811–1821. https://doi.org/10.1002/prot.26601

Studer, G., Tauriello, G., & Schwede, T. (2023). Assessment of the assessment—All about complexes. Proteins: Structure, Function and Bioinformatics, 91(12), 1850–1860. https://doi.org/10.1002/prot.26612

Kryshtafovych, A., Schwede, T., Topf, M., Fidelis, K., & Moult, J. (2023). Critical assessment of methods of protein structure prediction (CASP)—Round XV [Journal-article]. Proteins: Structure, Function, and Bioinformatics, 91(12), 1539–1549. https://doi.org/10.1002/prot.26617

Eberhardt, Jérôme, Lill, Markus, & Schwede, Torsten. (2023). Combining Bayesian optimization with sequence- or structure-based strategies for optimization of peptide-binding protein [Posted-content]. In ChemRxiv. American Chemical Society (ACS). https://doi.org/10.26434/chemrxiv-2023-b7l81

Robin, X., Leemann, M., Sagasta, A., Eberhardt, J., Schwede, T., & Durairaj, J. (2023). Automated benchmarking of combined protein structure and ligand conformation prediction [Posted-content]. Authorea. https://doi.org/10.22541/au.168382988.85108031/v1

Palermo, G., Accordi, G., Gadioli, D., Vitali, E., Silvano, C., Guindani, B., Ardagna, D., Beccari, A.R., Bonanni, D., Talarico, C., Lughini, F., Martinovic, J., Silva, P., Bohm, A., Beranek, J., Krenek, J., Jansik, B., Cosenza, B., Crisci, L., et al. (2023). Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach. Proceedings of the 20th ACM International Conference on Computing Frontiers 2023, CF 2023, 272–278. https://doi.org/10.1145/3587135.3592172

Alexander, Leila T, Durairaj, Janani, Kryshtafovych, Andriy, Abriata, Luciano A, Bayo, Yusupha, Bhabha, Gira, Breyton, Cécile, Caulton, Simon G, Chen, James, Degroux, Séraphine, Ekiert, Damian C, Erlandsen, Benedikte S, Freddolino, Peter L, Gilzer, Dominic, Greening, Chris, Grimes, Jonathan M, Grinter, Rhys, Gurusaran, Manickam, Hartmann, Marcus D, et al. (2023). Protein target highlights in CASP15: Analysis of models by structure providers. Proteins, 91(12), 1571–1599. https://doi.org/10.1002/prot.26545

Durairaj, Janani, Alexander, Leila Tamara, Studer, Gabriel, Tauriello, Gerardo, Prandi, Ingrid Guarnetti, Lepore, Rosalba, Chillemi, Giovanni, & Schwede, Torsten. (2023). From Genomes to Variant Interpretations Through Protein Structures. In SpringerBriefs in Applied Sciences and Technology (pp. 41–50). Springer Science and Business Media Deutschland GmbH. https://doi.org/10.1007/978-3-031-30691-4_6

Durairaj, Janani, Waterhouse, Andrew M., Mets, Toomas, Brodiazhenko, Tetiana, Abdullah, Minhal, Studer, Gabriel, Tauriello, Gerardo, Akdel, Mehmet, Andreeva, Antonina, Bateman, Alex, Tenson, Tanel, Hauryliuk, Vasili, Schwede, Torsten, & Pereira, Joana. (2023). Uncovering new families and folds in the natural protein universe. Nature, 622(7983), 646–653. https://doi.org/10.1038/s41586-023-06622-3

Kryshtafovych, Andriy, Antczak, Maciej, Szachniuk, Marta, Zok, Tomasz, Kretsch, Rachael C, Rangan, Ramya, Pham, Phillip, Das, Rhiju, Robin, Xavier, Studer, Gabriel, Durairaj, Janani, Eberhardt, Jerome, Sweeney, Aaron, Topf, Maya, Schwede, Torsten, Fidelis, Krzysztof, & Moult, John. (2023). New prediction categories in CASP15. Proteins, 91(12), 1550–1557. https://doi.org/10.1002/prot.26515

Marone, Romina, Landmann, Emmanuelle, Devaux, Anna, Lepore, Rosalba, Seyres, Denis, Zuin, Jessica, Burgold, Thomas, Engdahl, Corinne, Capoferri, Giuseppina, Dell’Aglio, Alessandro, Larrue, Clément, Simonetta, Federico, Rositzka, Julia, Rhiel, Manuel, Andrieux, Geoffroy, Gallagher, Danielle N., Schröder, Markus S., Wiederkehr, Amélie, Sinopoli, Alessandro, et al. (2023). Epitope-engineered human hematopoietic stem cells are shielded from CD123-targeted immunotherapy. Journal of Experimental Medicine, 220(12). https://doi.org/10.1084/jem.20231235

Robin, Xavier, Waterhouse, Andrew Mark, Bienert, Stefan, Studer, Gabriel, Alexander, Leila T., Tauriello, Gerardo, Schwede, Torsten, & Pereira, Joana. (2023). The SWISS-MODEL Repository of 3D Protein Structures and Models. In Open Access Databases and Datasets for Drug Discovery (pp. 175–199). wiley. https://doi.org/10.1002/9783527830497.ch6

Schweke, Hugo, Xu, Qifang, Tauriello, Gerardo, Pantolini, Lorenzo, Schwede, Torsten, Cazals, Frédéric, Lhéritier, Alix, Fernandez-Recio, Juan, Rodríguez-Lumbreras, Luis Angel, Schueler-Furman, Ora, Varga, Julia K., Jiménez-García, Brian, Réau, Manon F., Bonvin, Alexandre M. J. J., Savojardo, Castrense, Martelli, Pier-Luigi, Casadio, Rita, Tubiana, Jérôme, Wolfson, Haim J., et al. (2023). Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study. Proteomics, 23(17), e2200323. https://doi.org/10.1002/pmic.202200323

Vallat, Brinda, Tauriello, Gerardo, Bienert, Stefan, Haas, Juergen, Webb, Benjamin M., Zheng, Wei, Peisach, Ezra, Piehl, Dennis W., Anischanka, Ivan, Sillitoe, Ian, Tolchard, James, Varadi, Mihaly, Baker, David, Orengo, Christine, Zhang, Yang, Hoch, Jeffrey C., Kurisu, Genji, Patwardhan, Ardan, Velankar, Sameer, et al. (2023). ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models. Journal of Molecular Biology, 435(14), 168021. https://doi.org/10.1016/j.jmb.2023.168021

Alt, Silke, Haggstrom, Douglas, Kessmann, Helmut, Kloss, Florian, Schneider, Christian Elias, Jäger, Timo, Schwede, Torsten, Brakhage, Axel, & Dehio, Christoph. (2022). INCATE: a partnership to boost the antibiotic pipeline. Nature Reviews. Drug Discovery, 21(9), 621–622. https://doi.org/10.1038/d41573-022-00138-7

Landmann, Emmanuelle, Devaux, Anna, Lepore, Rosalba, Marone, Romina, Engdahl, Corinne, Hasiuk, Marko, Capoferri, Giuseppina, Wiederkehr, Amélie, Wellinger, Lisa C, Sinopoli, Alessandro, Do Sacramento, Valentin, Haydn, Anna, Garcia Prat, Laura, Divsalar, Christopher, Camus, Anna, Brault, Julie, Xu, Liwen, Schwede, Torsten, Porteus, Matthew H., et al. (2022). Engineered Single Amino Acid Substitutions Protect Hematopoietic Stem and Progenitor Cells from CD123 Targeted Immunotherapy [Journal-article]. Blood, 140(Supplement 1), 5724–5725. https://doi.org/10.1182/blood-2022-163815

Varadi, Mihaly, Nair, Sreenath, Sillitoe, Ian, Tauriello, Gerardo, Anyango, Stephen, Bienert, Stefan, Borges, Clemente, Deshpande, Mandar, Green, Tim, Hassabis, Demis, Hatos, Andras, Hegedus, Tamas, Hekkelman, Maarten L., Joosten, Robbie, Jumper, John, Laydon, Agata, Molodenskiy, Dmitry, Piovesan, Damiano, Salladini, Edoardo, et al. (2022). 3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources. GigaScience, 11, giac118. https://doi.org/10.1093/gigascience/giac118

Alexander, Leila T., Lepore, Rosalba, Kryshtafovych, Andriy, Adamopoulos, Athanassios, Alahuhta, Markus, Arvin, Ann M., Bomble, Yannick J., Böttcher, Bettina, Breyton, Cécile, Chiarini, Valerio, Chinnam, Naga Babu, Chiu, Wah, Fidelis, Krzysztof, Grinter, Rhys, Gupta, Gagan D., Hartmann, Marcus D., Hayes, Christopher S., Heidebrecht, Tatjana, Ilari, Andrea, et al. (2021). Target highlights in CASP14: analysis of models by structure providers. Proteins: Structure, Function, and Bioinformatics, 1–26. https://doi.org/10.1002/prot.26247

Kryshtafovych, Andriy, Schwede, Torsten, Topf, Maya, Fidelis, Krzysztof, & Moult, John. (2021). Critical assessment of methods of protein structure prediction (CASP)-Round XIV. Proteins: Structure, Function, and Bioinformatics, 89(12), 1607–1617. https://doi.org/10.1002/prot.26237

Mari, Alfredo, Roloff, Tim, Stange, Madlen, Søgaard, Kirstine K., Asllanaj, Erblin, Tauriello, Gerardo, Alexander, Leila Tamara, Schweitzer, Michael, Leuzinger, Karoline, Gensch, Alexander, Martinez, Aurélien E., Bielicki, Julia, Pargger, Hans, Siegemund, Martin, Nickel, Christian H., Bingisser, Roland, Osthoff, Michael, Bassetti, Stefano, Sendi, Parham, et al. (2021). Global Genomic Analysis of SARS-CoV-2 RNA Dependent RNA Polymerase Evolution and Antiviral Drug Resistance. Microorganisms, 9(5), 1094. https://doi.org/10.3390/microorganisms9051094

Pereira, Joana, & Schwede, Torsten. (2021). Interactomes in the era of deep learning. Science, 374(6573), 1319–1320. https://doi.org/10.1126/science.abm8295

Rehm, Heidi L., Page, Angela J. H., Smith, Lindsay, Adams, Jeremy B., Alterovitz, Gil, Babb, Lawrence J., Barkley, Maxmillian P., Baudis, Michael, Beauvais, Michael J. S., Beck, Tim, Beckmann, Jacques S., Beltran, Sergi, Bernick, David, Bernier, Alexander, Bonfield, James K., Boughtwood, Tiffany F., Bourque, Guillaume, Bowers, Sarion R., Brookes, Anthony J., et al. (2021). GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genomics, 1(2), 100029. https://doi.org/10.1016/j.xgen.2021.100029

Robin, Xavier, Haas, Juergen, Gumienny, Rafal, Smolinski, Anna, Tauriello, Gerardo, & 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), 1977–1986. https://doi.org/10.1002/prot.26213

Studer, Gabriel, Tauriello, Gerardo, Bienert, Stefan, Biasini, Marco, Johner, Niklaus, & Schwede, Torsten. (2021). ProMod3-A versatile homology modelling toolbox. PLoS Computational Biology, 17(1), e1008667. https://doi.org/10.1371/journal.pcbi.1008667

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. https://doi.org/10.3390/ijms21145152

Righetto, Ricardo D., Anton, Leonie, Adaixo, Ricardo, Jakob, Roman P., Zivanov, Jasenko, Mahi, Mohamed-Ali, Ringler, Philippe, Schwede, Torsten, Maier, Timm, & Stahlberg, Henning. (2020). High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica. Nature Communications, 11(1), 5101. https://doi.org/10.1038/s41467-020-18870-2

Righetto, Ricardo D., Anton, Leonie, Adaixo, Ricardo, Jakob, Roman P., Zivanov, Jasenko, Mahi, Mohamed-Ali, Ringler, Philippe, Schwede, Torsten, Maier, Timm, & Stahlberg, Henning. (2020). Author Correction: High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica. Nature Communications, 11(1), 5873. https://doi.org/10.1038/s41467-020-19845-z

Kryshtafovych, A., Schwede, T., Topf, M., Fidelis, K., & Moult, J. (2019). Cover Image, Volume 87, Issue 12 [Journal-article]. Proteins: Structure, Function, and Bioinformatics, 87(12). https://doi.org/10.1002/prot.25565

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., et al. (2019). Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure (London, England : 1993), 27(12), 1745–1759. https://doi.org/10.1016/j.str.2019.11.002

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. https://doi.org/10.1002/prot.25767

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. https://doi.org/10.1002/prot.25815

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. https://doi.org/10.1002/prot.25823

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., et al. (2019). Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins: Structure, Function, and Bioinformatics, 87(12), 1037–1057. https://doi.org/10.1002/prot.25805

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. https://doi.org/10.1093/bioinformatics/btz828

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. https://doi.org/10.1007/978-1-4939-8736-8_17

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. https://doi.org/10.1002/prot.25431

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, et al. (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. https://doi.org/10.1002/prot.25392

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. https://doi.org/10.1002/prot.25425

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. https://doi.org/10.1002/prot.25408

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. https://doi.org/10.1002/prot.25406

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. https://doi.org/10.1002/prot.25415

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. https://doi.org/10.1093/nar/gky427

Capella-Gutierrez, Salvador, Iglesia, Diana de la, Haas, Juergen, Lourenco, Analia, Fernández, José María, Repchevsky, Dmitry, Dessimoz, Christophe, Schwede, Torsten, Notredame, Cedric, Gelpi, Josep Ll, & Valencia, Alfonso. (2017). Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking [Posted-content]. In bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/181677

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. https://doi.org/10.1038/s41598-017-09654-8

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. https://doi.org/10.1093/nar/gkw1132

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. https://doi.org/10.1016/j.str.2017.08.001

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. https://doi.org/10.1021/acs.jchemed.6b00596

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, et al. (2017). Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome Medicine, 9(1), 113. https://doi.org/10.1186/s13073-017-0509-y

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, et al. (2017). Exome sequencing of healthy phenotypic extremes links TROVE2 to emotional memory and PTSD. Nature Human Behaviour, 1, 81. https://doi.org/10.1038/s41562-017-0081

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. https://doi.org/10.1002/prot.25371

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. https://doi.org/10.1186/s13104-017-2428-9

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. https://doi.org/10.1128/mbio.00294-17

Thornton, Janet M., Valencia, Alfonso, & Schwede, Torsten. (2017). Anna Tramontano 1957-2017. Nature Structural and Molecular Biology, 24(5), 431–432. https://doi.org/10.1038/nsmb.3410

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., et al. (2017). 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallographica Section D, 73(Pt 9), 710–728. https://doi.org/10.1107/s2059798317011597

Kryshtafovych A, Barbato A, Monastyrskyy B, Fidelis K, Schwede T, & Tramontano A. (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(S1), 349–369. https://doi.org/10.1002/prot.24919

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: Structure, Function, and Bioinformatics, 84 Suppl 1(1), 69–349. https://doi.org/10.1002/prot.24919

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., et al. (2016). Some of the most interesting CASP11 targets through the eyes of their authors. Proteins: Structure, Function, and Bioinformatics, 84(Suppl 1), 34–50. https://doi.org/10.1002/prot.24942

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. https://doi.org/10.1002/prot.25064

Goldenberger, Daniel, Schwede, Torsten, Page, Malcolm, & Creus, Marc. (2016). Plasmid-mediated colistin resistance in a patient infected with Klebsiella pneumoniae [Review of Plasmid-mediated colistin resistance in a patient infected with Klebsiella pneumoniae]. The Lancet Infectious Diseases, 16, Article 9. https://doi.org/10.1016/s1473-3099(16)30197-9

Studer, G., Jakob, R. P., Mahi, M. A., Wiesand, U., Schwede, T., & Maier, T. (2016). Crystal structure of urease from Yersinia enterocolitica (Studer, Gabriel, Ed.) [dataset]. Worldwide Protein Data Bank. https://doi.org/10.2210/pdb4z42/pdb

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(Pt 1), 45–58. https://doi.org/10.1107/s2052252514023306

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. https://doi.org/10.1098/rsob.140227

Sali, Andrej, Berman, Helen M., Schwede, Torsten, Trewhella, Jill, Kleywegt, Gerard, Burley, Stephen K., Markley, John, Nakamura, Haruki, Adams, Paul, Bonvin, Alexandre M. J. J., Chiu, Wah, Peraro, Matteo Dal, Di Maio, Frank, Ferrin, Thomas E., Grünewald, Kay, Gutmanas, Aleksandras, Henderson, Richard, Hummer, Gerhard, Iwasaki, Kenji, et al. (2015). Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure: With Folding and Design, 23(7), 67–1156. https://doi.org/10.1016/j.str.2015.05.013

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(Web Server issue), W252–8. https://doi.org/10.1093/nar/gku340

Gallo Cassarino, Tiziano, Bordoli, Lorenza, & Schwede, Torsten. (2014). Assessment of ligand binding site predictions in CASP10. Proteins, 82 Suppl 2(S2), 63–154. https://doi.org/10.1002/prot.24495

Haas, Jürgen, & Schwede, Torsten. (2014). Unabhängige Validierung von Methoden zur Proteinstrukturvorhersage. Biospektrum, 20(2), 236–237. https://doi.org/10.1007/s12268-014-0432-3

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), 26–112. https://doi.org/10.1002/prot.24347

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, et al. (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. https://doi.org/10.1002/prot.24489

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. https://doi.org/10.1002/prot.24452

Schmidt, Tobias, Bergner, Andreas, & Schwede, Torsten. (2014). Modelling three-dimensional protein structures for applications in drug design. Drug Discovery Today, 19(7), 7–890. https://doi.org/10.1016/j.drudis.2013.10.027

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. https://doi.org/10.1021/jp5028564

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, et al. (2014). Fifteen years SIB Swiss Institute of Bioinformatics : life science databases, tools and support. Nucleic Acids Research, 42(Web Server issue), W436–41. https://doi.org/10.1093/nar/gku380

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. https://doi.org/10.1093/bioinformatics/btu457

Uda, Narasimha Rao, Upert, Grégory, Angelici, Gaetano, Schmidt, Tobias, Schwede, Torsten, & 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), 88–95. https://doi.org/10.1039/c3mt00125c

Schwede, Torsten. (2013). Homology Modeling of Protein Structures. In Roberts, G.C.K. (Ed.), Encyclopedia of Biophysics (pp. 992–998). Springer. https://doi.org/10.1007/978-3-642-16712-6_417

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(Pt 5), 9–701. https://doi.org/10.1107/s0907444913007051

Haas, Juergen, Roth, Steven, Arnold, Konstantin, Kiefer, Florian, Schmidt, Tobias, Bordoli, Lorenza, & Schwede, Torsten. (2013). The Protein Model Portal: a comprehensive resource for protein structure and model information. Database, 2013, bat031. https://doi.org/10.1093/database/bat031

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), 8–2722. https://doi.org/10.1093/bioinformatics/btt473

Schwede, Torsten. (2013). Protein modeling: what happened to the “protein structure gap”? Structure: With Folding and Design, 21(9), 1531–1540. https://doi.org/10.1016/j.str.2013.08.007

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), 81–875. https://doi.org/10.1016/j.str.2013.04.020

Bordoli, Lorenza, & Schwede, Torsten. (2012). Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal. In Orry, Andrew JW; Abagyan, Ruben (Ed.), Homology Modeling: Methods and Protocols: Vol. Vol. 857 (p. S. 107–36). Humana Press. https://doi.org/10.1007/978-1-61779-588-6_5

Barbato, Alessandro, Benkert, Pascal, Schwede, Torsten, Tramontano, Anna, & Kosinski, Jan. (2012). Improving your target-template alignment with MODalign. Bioinformatics, 28(7), 9–1038. https://doi.org/10.1093/bioinformatics/bts070

Schwede, Torsten, & Iber, Dagmar. (2012). ECCB 2012 : The 11th European Conference on Computational Biology [Review of ECCB 2012 : The 11th European Conference on Computational Biology]. Bioinformatics, 28, Article 18. https://doi.org/10.1093/bioinformatics/bts490