Biblio
Found 28 results
Filters: Author is Caflisch, A. and Keyword is molecular dynamics [Clear All Filters]
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2025. A FAIR-compliant management solution for molecular simulation trajectories. Journal of Chemical Information and Modeling. XXX(YYY)
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2023. Disrupting dimeric β-amyloid by electric fields. ACS Physical Chemistry Au. 3(5):456–466.
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2023. Optimized reaction coordinates for analysis of enhanced sampling. The Journal of Chemical Physics. 159(1):015101-24.
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2023. Structure-based design of inhibitors of the m6A‑RNA writer enzyme METTL3. ACS Bio & Med Chem Au. 3(4):359–370.
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2022. Structure-based design of ligands of the m6A-RNA reader YTHDC1. European Journal of Medicinal Chemistry Reports. 5:100057.
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2020. Kinetic control of amyloidogenesis calls for unconventional drugs to fight Alzheimer's disease. ACS Chemical Neuroscience. 11(2):103-104.
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2020. SAPPHIRE-based clustering. Journal of Chemical Theory and Computation. 16(10):6383–6396.
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2019. The 3A6-TCR/superagonist/HLA-DR2a complex shows similar interface and reduced flexibility compared to the complex with self-peptide. Proteins: Structure, Function, and Bioinformatics. 88(1):31-46.
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2019. Flexible binding of m6A reader protein YTHDC1 to its preferred RNA motif. Journal of Chemical Theory and Computation. 15(12):7004-7014.
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2018. Protein structure-based drug design: From docking to molecular dynamics. Current Opinion in Structural Biology. 48:93-102.
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2018. Structure-based discovery of selective BRPF1 bromodomain inhibitors. European Journal of Medicinal Chemistry. (155):337-352.
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2017. Amyloid β fibril elongation by monomers involves disorder at the tip. Journal of Chemical Theory and Computation. 13(10):5117-5130.
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2017. Focused conformational sampling in proteins.. Journal of Chemical Physics. 147(19):195102.
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2017. Reducing the flexibility of type II dehydroquinase for inhibition: A fragment-based approach and molecular dynamics study. ChemMedChem. 12(18):1512-1524.
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2015. Evolutionary conserved Tyr169 stabilizes the β2-α2 loop of the prion protein. Journal of the American Chemical Society. 137(8):2948-2957.
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2015. A molecular simulation protocol to avoid sampling redundancy and discover new states. Biochimica et Biophysica Acta (BBA) - General Subjects. 1850(5):889-902.
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2015. Peptide binding to a PDZ domain by electrostatic steering via nonnative salt bridges. Biophysical Journal. 108(9):2362-2370.
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2015. Structure-based drug design identifies polythiophenes as antiprion compounds. Science Translational Medicine. 7(299):299ra123.
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2014. High-resolution visualisation of the states and pathways sampled in molecular dynamics simulations. Scientific Reports. 4:6264.
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2014. Spontaneous self-assembly of engineered armadillo repeat protein fragments into a folded structure. Structure. 22(7):985-995.
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2013. Mechanism and kinetics of acetyl-lysine binding to bromodomains. Journal of Chemical Theory and Computation. 9(9):4225-4232.
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2012. 50 years of Lifson–Roig models: Application to molecular simulation data. Journal of Chemical Theory and Computation. 8(1):363-373.
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2012. Efficient construction of mesostate networks from molecular dynamics trajectories. Journal of Chemical Theory and Computation. 8(2):1108-1120.
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2012. Free energy guided sampling. Journal of Chemical Theory and Computation. 8(6):2134-2140.
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2012. Mechanisms and kinetics of amyloid aggregation investigated by a phenomenological coarse-grained model. Computational Modeling of Biological Systems: Modeling Macromolecular Assemblies. :191-214.