Publications Caflisch Group

ZORA Publication List

Publications

• 2025

  • Vitalis, Andreas; Parker, David; Radler, Fabian; Vargas-Rosales, Pablo Andrés; Zhang, Yang; Marchand, Jean-Rémy; Caflisch, Amedeo (2025). Parallelized Tools for the Preparation and Curation of Large Libraries for Virtual Screening. Journal of Computational Chemistry, 46(7):e70074.
  • Vitalis, Andreas; Winkler, Steffen; Zhang, Yang; Widmer, Julian; Caflisch, Amedeo (2025). A FAIR-Compliant Management Solution for Molecular Simulation Trajectories. Journal of Chemical Information and Modeling, 65(5):2443-2455.
  • Vargas-Rosales, Pablo Andrés; Caflisch, Amedeo (2025). The physics-AI dialogue in drug design. RSC Medicinal Chemistry:Epub ahead of print.

• 2024

  • Widmer, Julian; Vitalis, Andreas; Caflisch, Amedeo (2024). On the specificity of the recognition of m6A-RNA by YTH reader domains. Journal of Biological Chemistry, 300(12):107998.
  • Tarullo, Marco; Fernandez Rodriguez, Guillermo; Iaiza, Alessia; Venezia, Sara; Macone, Alberto; Incocciati, Alessio; Masciarelli, Silvia; Marchioni, Marcella; Giorgis, Marta; Lolli, Marco Lucio; Fornaseri, Federico; Proietti, Ludovica; Grebien, Florian; Rosignoli, Serena; Paiardini, Alessandro; Rotili, Dante; Mai, Antonello; Bochenkova, Elena; Caflisch, Amedeo; Fazi, Francesco; Fatica, Alessandro (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.
  • Cazzanelli, Giulia; Dalle Vedove, Andrea; Sbardellati, Nicolo; Valer, Luca; Caflisch, Amedeo; Lolli, Graziano (2024). Enhanced cellular death in liver and breast cancer cells by dual BET/BRPF1 inhibitors. Protein Science, 33(11):e5191.
  • Hwang, Wonmuk; Austin, Steven L; Blondel, Arnaud; Boittier, Eric D; Boresch, Stefan; Buck, Matthias; Buckner, Joshua; Caflisch, Amedeo; Chang, Hao-Ting; Cheng, Xi; Choi, Yeol Kyo; Chu, Jhih-Wei; Crowley, Michael F; Cui, Qiang; Damjanovic, Ana; Deng, Yuqing; Devereux, Mike; Ding, Xinqiang; Feig, Michael F; Gao, Jiali; Glowacki, David R; Gonzales, James E; Hamaneh, Mehdi Bagerhi; Harder, Edward D; Hayes, Ryan L; Huang, Jing; Huang, Yandong; Hudson, Phillip S; Im, Wonpil; Islam, Shahidul M; et al (2024). CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. Journal of Physical Chemistry B, 128(41):9976-10042.
  • Cheng-Sánchez, Iván; Gosselé, Katherine; Palaferri, Leonardo; Laul, Eleen; Riccabella, Gionata; Bedi, Rajiv K; Li, Yaozong; Müller, Anna; Corbeski, Ivan; Caflisch, Amedeo; Nevado, Cristina (2024). Structure-Based Design of CBP/EP300 Degraders: When Cooperativity Overcomes Affinity. JACS Au, 4(9):3466-3474.
  • Zhou, Jiangtao; Assenza, Salvatore; Tatli, Meltem; Tian, Jiawen; Ilie, Ioana M; Starostin, Eugene L; Caflisch, Amedeo; Knowles, Tuomas P J; Dietler, Giovanni; Ruggeri, Francesco S; Stahlberg, Henning; Sekatskii, Sergey K; Mezzenga, Raffaele (2024). Hierarchical Protofilament Intertwining Rules the Formation of Mixed-Curvature Amyloid Polymorphs. Advanced Science, 11(32):e2402740.
  • Zálešák, František; Nai, Francesco; Herok, Marcin; Bochenkova, Elena; Bedi, Rajiv K; Li, Yaozong; Errani, Francesco; Caflisch, Amedeo (2024). Structure-Based Design of a Potent and Selective YTHDC1 Ligand. Journal of Medicinal Chemistry, 67(11):9516-9535.
  • Nai, Francesco; Flores Espinoza, Maria Paula; Invernizzi, Annalisa; Vargas-Rosales, Pablo Andrés; Bobileva, Olga; Herok, Marcin; Caflisch, Amedeo (2024). Small-Molecule Inhibitors of the m7G-RNA Writer METTL1. ACS Bio & Med Chem Au, 4(2):100-110.
  • Corbeski, Ivan; Vargas-Rosales, Pablo Andrés; Bedi, Rajiv Kumar; Deng, Jiahua; Coelho, Dylan; Braud, Emmanuelle; Iannazzo, Laura; Li, Yaozong; Huang, Danzhi; Ethève-Quelquejeu, Mélanie; Cui, Qiang; Caflisch, Amedeo (2024). The catalytic mechanism of the RNA methyltransferase METTL3. eLife, 12:RP92537.
  • Errani, Francesco; Invernizzi, Annalisa; Herok, Marcin; Bochenkova, Elena; Stamm, Fiona; Corbeski, Ivan; Romanucci, Valeria; Di Fabio, Giovanni; Zálešák, František; Caflisch, Amedeo (2024). Proteolysis Targeting Chimera Degraders of the METTL3-14 m$^{6}$A-RNA Methyltransferase. JACS Au, 4(2):713-729.

• 2023

  • Bobrovs, Raitis; Drunka, Laura; Kanepe, Iveta; Jirgensons, Aigars; Caflisch, Amedeo; Salvalaglio, Matteo; Jaudzems, Kristaps (2023). Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors. Journal of Chemical Information and Modeling, 63(21):6890-6899.
  • Cazzanelli, Giulia; Dalle Vedove, Andrea; Parolin, Eleonora; D'Agostino, Vito Giuseppe; Unzue, Andrea; Nevado, Cristina; Caflisch, Amedeo; Lolli, Graziano (2023). Reevaluation of bromodomain ligands targeting BAZ2A. Protein Science, 32(9):e4752.
  • Vargas-Rosales, Pablo Andrés; D'Addio, Alessio; Zhang, Yang; Caflisch, Amedeo (2023). Disrupting Dimeric β-Amyloid by Electric Fields. ACS Physical Chemistry Au, 3(5):456-466.
  • Widmer, Julian; Langini, Cassiano; Vitalis, Andreas; Caflisch, Amedeo (2023). Optimized reaction coordinates for analysis of enhanced sampling. Journal of Chemical Physics, 159(1):015101.
  • Bedi, Rajiv Kumar; Huang, Danzhi; Li, Yaozong; Caflisch, Amedeo (2023). Structure-Based Design of Inhibitors of the m$^{6}$A-RNA Writer Enzyme METTL3. ACS Bio & Med Chem Au, 3(4):359-370.
  • Ilie, Ioana M; Ehrhardt, Claus; Caflisch, Amedeo; Weitz-Schmidt, Gabriele (2023). Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations. Journal of Chemical Information and Modeling, 63(12):3878-3891.
  • Reimann, Regina R; Puzio, Martina; Rosati, Antonella; Emmenegger, Marc; Schneider, Bernard L; Valdés, Pamela; Huang, Danzhi; Caflisch, Amedeo; Aguzzi, Adriano (2023). Rapid ex vivo reverse genetics identifies the essential determinants of prion protein toxicity. Brain Pathology, 33(2):e13130.
  • Xiang, Yusen; Zhai, Guanglei; Li, Yaozong; Wang, Mengge; Chen, Xixiang; Wang, Ruyu; Xie, Hang; Zhang, Weidong; Ge, Guangbo; Zhang, Qian; Xu, Yechun; Caflisch, Amedeo; Xu, Jianrong; Chen, Hongzhuan; Chen, Lili (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.

Pagination