Browse by Basel Contributors ID

Group by: Date | Item Type | Refereed | No Grouping

Article

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.

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.

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.

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.

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.

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.

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.

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.

Preprint

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.

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.