Biblio

Found 308 results
2025
Zhang Y., Vitalis A..  2025.  Benchmarking the robustness of the correct identification of flexible 3D objects using common machine learning models. Patterns. 6(1):101147.
Invernizzi A., Nai F., Bedi R.K, Vargas-Rosales P.A, Li Y., Bochenkova E., Herok M., Zálešák F., Caflisch A..  2025.  Discovery of YTHDF2 Ligands by Fragment-Based Design. ACS Bio & Med Chem Au. X(X)
Vargas-Rosales P.A, Giangreco G., Caflisch A..  2025.  Disrupting Amyloid Filaments of Tau by Means of Electric Fields.. The Journal of Physical Chemistry B. 129(36):9124-9137.
Vitalis A., Winkler S., Zhang Y., Widmer J., Caflisch A..  2025.  A FAIR-compliant management solution for molecular simulation trajectories. Journal of Chemical Information and Modeling. 65(5):2443-2455.
Vitalis A., Parker D., Radler F., Vargas-Rosales P.A, Zhang Y., Marchand J.-R., Caflisch A..  2025.  Parallelized tools for the preparation and curation of large libraries for virtual screening. Journal of Computational Chemistry. 46(7)
Vargas-Rosales P.A, Caflisch A..  2025.  The Physics-AI dialogue in drug design. RSC Medicinal Chemistry.
Zhang S., Liu S., Lai H., Bender K.W, Kim G., Caflisch A., Zipfel C..  2025.  Reverse Engineering of the Pattern Recognition Receptor FLS2 Reveals Key Design Principles of Broader Recognition Spectra against Evading flg22 Epitopes. Nature Plants.
Gosselé K., Latino I., Laul E., Kirillova M.S, Pascanu V., Carloni E., Bedi R.K, Pizzichetti C., Caflisch A., González S.F et al..  2025.  Selective CBP/EP300 Bromodomain Inhibitors: Novel Epigenetic Tools to Counter TNF-α-Driven Inflammation. Journal of the American Chemical Society Au. 5:2491-2499.
2024
AIMS A, Caflisch A..  2024.  AI is a viable alternative to high throughput screening: a 318-target study.. Scientific Reports. 14(1):7526.
Corbeski I., Vargas-Rosales P.A, Bedi R.K, Deng J., Coelho D., Braud E., Iannazzo L., Li Y., Huang D., Ethève-Quelquejeu M. et al..  2024.  The catalytic mechanism of the RNA methyltransferase METTL3. eLife. 12:RP92537.
Hwang W., Austin S.L, Blondel A., Boittier E.D, Boresch S., Buck M., Buckner J., Caflisch A., Chang H., Cheng X. et al..  2024.  CHARMM at 45: Enhancements in accessibility, functionality, and speed.. The Journal of Physical Chemistry B. X
Cazzanelli G., A. Vedove D, Sbardellati N., Valer L., Caflisch A., Lolli G..  2024.  Enhanced cellular death in liver and breast cancer cells by dual BET/BRPF1 inhibitors. Protein Science. 33(11):e5191.
Zhou J., Assenza S., Tatli M., Tian J., Ilie I.M, Starostin E., Caflisch A., Knowles T., Dietler G., Ruggeri F. et al..  2024.  Hierarchical protofilament intertwining rules the formation of mixed-curvature amyloid polymorphs. Advanced Science. 11:e2402740.
Tarullo M., G. Rodriguez F, Iaiza A., Venezia S., Macone A., Incocciati A., Masciarelli S., Marchioni M., Giorgis M., Lolli M. et al..  2024.  Off-target inhibition of human dihydroorotate dehydrogenase (hDHODH) highlights challenges in the development of fat mass and obesity-associated protein (FTO) inhibitors. ACS Pharmacology & Translational Science. 7(12):4096-4111.
Errani F., Invernizzi A., Herok M., Bochenkova E., Stamm F., Corbeski I., Romanucci V., Di Fabio G., Zálešák F., Caflisch A..  2024.  Proteolysis targeting chimera degraders of the METTL3–14 m6A-RNA methyltransferase. Journal of the American Chemical Society Au. 4(2):713-729.
Widmer J., Vitalis A., Caflisch A..  2024.  On the specificity of the recognition of m6A-RNA by YTH reader domains. The Journal of Biological Chemistry. 300(12):107998.
Zálešák F., Nai F., Herok M., Bochenkova E., Bedi R.K, Li Y., Errani F., Caflisch A..  2024.  Structure-based design of a potent and selective YTHDC1 ligand. Journal of Medicinal Chemistry. 67(11):9516-9535.
Cheng-Sánchez I., Gosselé K., Palaferri L., Laul E., Riccabella G., Bedi R.K, Li Y., Müller A., Corbeski I., Caflisch A. et al..  2024.  Structure-based design of CBP/EP300 degraders: when cooperativity overcomes affinity. Journal of the American Chemical Society Au. 4(9):3466-3474.
2023
Ilie I.M, Ehrhardt C., Caflisch A., Weitz-Schmidt G..  2023.  Decrypting Integrins by mixed-solvent molecular dynamics simulations. Journal of Chemical Information and Modeling. 63:3878–3891.
Vargas-Rosales P.A, DAddio A., Zhang Y., Caflisch A..  2023.  Disrupting dimeric β-amyloid by electric fields. ACS Physical Chemistry Au. 3(5):456–466.
Bobrovs R., Drunka L., Kaņepe I., Jirgensons A., Caflisch A., Salvalaglio M., Jaudzems K..  2023.  Exploring the binding pathway of novel non-peptidomimetic plasmepsin V inhibitors. Journal of Chemical Information and Modeling. 63(21):6890-6899.
Xiang Y., Zhai G., Li Y., Wang M., Chen X., Wang R., Xie H., Zhang W., Ge G., Zhang Q. et al..  2023.  Ginkgolic acids inhibit SARS-CoV-2 and its variants by blocking the spike protein/ACE2 interplay. International Journal of Biological Macromolecules. 226:780-792.
A. Vedove D, Cazzanelli G., Corsi J., Sedykh M., Batiste L., Marchand J.-R., Spiliotopoulos D., D'Agostino V.G., Caflisch A., Lolli G..  2023.  Identification of BAZ2A bromodomain hit compounds. Acta Crystallographica Section A: Foundations of Crystallography. 78(X):a418-a418.
Widmer J., Langini C., Vitalis A., Caflisch A..  2023.  Optimized reaction coordinates for analysis of enhanced sampling. The Journal of Chemical Physics. 159(1):015101-24.
Reimann R.R, Puzio M., Rosati A., Emmenegger M., Schneider B.L, Valdés P., Huang D., Caflisch A., Aguzzi A..  2023.  Rapid ex vivo reverse genetics identifies the essential determinants of prion protein toxicity. Brain Pathology. 33(2):e13130.

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