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Selected Publications

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

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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

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URLs

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

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Selected Projects & Collaborations

The Protein Universe Atlas

Research Project | 3 Project Members

The term "protein universe" refers to the collection of all possible proteins that can be constructed from the small alphabet of 22 proteinogenic amino acids1,2. In this representation, functionally characterised proteins correspond to stars, protein families to galaxies, and protein superfamilies to clusters of galaxies, surrounded by all those sequences which are evolutionary related but not hitherto functionally characterised or sampled by nature. In this project, we will develop a new web service to navigate through the landscape of this universe that is currently covered by all catalogued natural proteins - the "Protein Universe Atlas". We will apply deep learning protein language models (pLMs) and abstract protein structure representations to model this landscape in three dimensions (3D), providing users with an interactive and integrative platform that will facilitate the annotation, biocuration and further study of a protein, a set of proteins, or all proteins catalogued so far.

LIGATE - Ligand Generator and portable drug discovery platform AT Exascale

Research Project | 6 Project Members

LIGATE is an EU funded project that aims to integrate and co-design best in class European components on Computer-Aided Drug Design (CADD) solutions exploiting today high-end supercomputer and tomorrow Exascale resources. The implementation of machine learning, extreme scale computer simulations, and big data analytics in the drug design and development process offer an excellent opportunity to lower the risk of investment and reduce the time to patient. The availability of powerful computing resources, new numerical models for simulations, and artificial intelligence increase the accuracy and predictability of CADD, reducing the costs and time for the design and the production of novel drugs.

The SWISS-MODEL expert system for comparative protein structure modeling

Research Project | 6 Project Members

SWISS-MODEL is a web-based expert system dedicated to protein structure homology modeling. Homology modeling is currently the most accurate method to generate reliable three-dimensional protein structure models and is routinely used in many practical applications. Homology (or comparative) modeling methods make use of experimental protein structures ("templates") to build models for evolutionary related proteins ("targets"). SWISS-MODEL is one of the most widely used web-based modeling servers with nearly one million model requests annually. The SWISS-MODEL Workspace provides a personal working environment where the user can carry out several modeling projects in parallel. The necessary resources, i.e. up-to-date protein sequence and structure databases and specialized tools for template selection, model building and structure quality evaluation are accessible using a web interface. Currently, the system supports more than 250'000 registered users. The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modeling pipeline. The aim of the SWISS-MODEL Repository is to provide access to an up-to-date collection of annotated 3D protein models for human proteins and a set of relevant models organisms. The Repository allows the users to assess the quality of the models in the database, search for alternative template structures, and to build models interactively via SWISS-MODEL Workspace. The SWISS-MODEL Repository is tightly integrated with external resources such as UniProt, InterPro and STRING databases. The services of the SWISS-MODEL expert system are available at http://swissmodel.expasy.org/ SWISS-MODEL is supported by the SIB Swiss Institute of Bioinformatics.