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Caflisch
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Publications
2024
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.
2022
Ilie, Ioana M; Caflisch, Amedeo (2022).
Antibody binding increases the flexibility of the prion protein.
BBA - Proteins and Proteomics, 1870(11-12):140827.
Dehabadi, Maryam Haji; Caflisch, Amedeo; Ilie, Ioana M; Firouzi, Rohoullah (2022).
Interactions of Curcumin's Degradation Products with the Aβ$_{42}$ Dimer: A Computational Study.
Journal of Physical Chemistry B, 126(39):7627-7637.
Vargas-Rosales, Pablo Andrés; Caflisch, Amedeo (2022).
Domino Effect in Allosteric Signaling of Peptide Binding.
Journal of Molecular Biology, 434(17):167661.
Nai, Francesco; Nachawati, Raed; Zálešák, František; Wang, Xiang; Li, Yaozong; Caflisch, Amedeo (2022).
Fragment Ligands of the m$^{6}$A-RNA Reader YTHDF2.
ACS Medicinal Chemistry Letters, 13(9):1500-1509.
Dalle Vedove, Andrea; Cazzanelli, Giulia; Batiste, Laurent; Marchand, Jean-Rémy; Spiliotopoulos, Dimitrios; Corsi, Jessica; D'Agostino, Vito Giuseppe; Caflisch, Amedeo; Lolli, Graziano (2022).
Identification of a BAZ2A-Bromodomain Hit Compound by Fragment Growing.
ACS Medicinal Chemistry Letters, 13(9):1434-1443.
Ilie, Ioana M; Bacci, Marco; Vitalis, Andreas; Caflisch, Amedeo (2022).
Antibody binding modulates the dynamics of the membrane-bound prion protein..
Biophysical Journal, 121(14):2813-2825.
García-Viñuales, Sara; Ilie, Ioana M; Santoro, Anna Maria; Romanucci, Valeria; Zarrelli, Armando; Di Fabio, Giovanni; Caflisch, Amedeo; Milardi, Danilo (2022).
Silybins inhibit human IAPP amyloid growth and toxicity through stereospecific interactions.
BBA - Proteins and Proteomics, 1870(5):140772.
Nass, Karol J; Ilie, Ioana M; Saller, Manfred J; Driessen, Arnold J M; Caflisch, Amedeo; Kammerer, Richard A; Li, Xiaodan (2022).
The role of the N-terminal amphipathic helix in bacterial YidC: Insights from functional studies, the crystal structure and molecular dynamics simulations.
Biochimica et biophysica acta. Biomembranes, 1864(3):183825.
Salutari, Ilaria; Caflisch, Amedeo (2022).
Dynamics of the Histone Acetyltransferase Lysine-Rich Loop in the Catalytic Core of the CREB-Binding Protein.
Journal of Chemical Information and Modeling, 62(4):1014-1024.
Schilling, Johannes; Jost, Christian; Ilie, Ioana Mariuca; Schnabl, Joachim; Buechi, Oralea; Eapen, Rohan S; Truffer, Rafaela; Caflisch, Amedeo; Forrer, Patrik (2022).
Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs.
Journal of Biological Chemistry, 298(1):101403.
Cocina, Francesco; Vitalis, Andreas; Caflisch, Amedeo (2022).
Spiking burstiness and working memory in the human medial temporal lobe.
Cerebral Cortex Communications, 3(4):tgac039.
Giordano, Deborah; Langini, Cassiano; Caflisch, Amedeo; Marabotti, Anna; Facchiano, Angelo (2022).
Molecular dynamics analysis of the structural properties of the transglutaminases of Kutzneria albida and Streptomyces mobaraensis.
Computational and Structural Biotechnology Journal, 20:3924-3934.
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