Publications of the Caflisch Group
ZORA Publication List
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Publications
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2023
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Exploring the Binding Pathway of Novel Nonpeptidomimetic Plasmepsin V Inhibitors. Journal of Chemical Information and Modeling, 63(21):6890-6899.
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Reevaluation of bromodomain ligands targeting BAZ2A. Protein Science, 32(9):e4752.
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Disrupting Dimeric β-Amyloid by Electric Fields. ACS Physical Chemistry Au, 3(5):456-466.
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Optimized reaction coordinates for analysis of enhanced sampling. Journal of Chemical Physics, 159(1):015101.
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Structure-Based Design of Inhibitors of the m$^{6}$A-RNA Writer Enzyme METTL3. ACS Bio & Med Chem Au, 3(4):359-370.
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Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations. Journal of Chemical Information and Modeling, 63(12):3878-3891.
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Rapid ex vivo reverse genetics identifies the essential determinants of prion protein toxicity. Brain Pathology, 33(2):e13130.
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Ginkgolic acids inhibit SARS-CoV-2 and its variants by blocking the spike protein/ACE2 interplay. International Journal of Biological Macromolecules, 226:780-792.
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2022
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Antibody binding increases the flexibility of the prion protein. BBA - Proteins and Proteomics, 1870(11-12):140827.
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Interactions of Curcumin's Degradation Products with the Aβ$_{42}$ Dimer: A Computational Study. Journal of Physical Chemistry B, 126(39):7627-7637.
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Domino Effect in Allosteric Signaling of Peptide Binding. Journal of Molecular Biology, 434(17):167661.
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Fragment Ligands of the m$^{6}$A-RNA Reader YTHDF2. ACS Medicinal Chemistry Letters, 13(9):1500-1509.
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Identification of a BAZ2A-Bromodomain Hit Compound by Fragment Growing. ACS Medicinal Chemistry Letters, 13(9):1434-1443.
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Antibody binding modulates the dynamics of the membrane-bound prion protein.. Biophysical Journal, 121(14):2813-2825.
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Silybins inhibit human IAPP amyloid growth and toxicity through stereospecific interactions. BBA - Proteins and Proteomics, 1870(5):140772.
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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.
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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.
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Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. Journal of Biological Chemistry, 298(1):101403.
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Spiking burstiness and working memory in the human medial temporal lobe. Cerebral Cortex Communications, 3(4):tgac039.
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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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2021
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Identification of a BAZ2A Bromodomain Hit Compound by Fragment Joining. ACS Bio & Med Chem Au, 1(1):5-10.
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METTL3 Inhibitors for Epitranscriptomic Modulation of Cellular Processes. ChemMedChem, 16(19):3035-3043.
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1,4,9-Triazaspiro[5.5]undecan-2-one Derivatives as Potent and Selective METTL3 Inhibitors. Journal of Medicinal Chemistry, 64(17):12738-12760.
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Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation. Molecular Cell, 81(16):3368-3385.e9.
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Combined computational and cellular screening identifies synergistic inhibition of SARS-CoV-2 by lenvatinib and remdesivir. Journal of General Virology, 102(7):001625.
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Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes. Chemical Reviews, 121(3):1845-1893.
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Atomistic and Thermodynamic Analysis of N6-Methyladenosine (m 6 A) Recognition by the Reader Domain of YTHDC1. Journal of Chemical Theory and Computation, 17(2):1240-1249.
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Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ. Cell, 184(2):545-559.e22.
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Flanking sequence preference modulates de novo DNA methylation in the mouse genome. Nucleic Acids Research, 49(1):145-157.
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