Publications of the Caflisch Group
ZORA Publication List
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Publications
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2019
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Flexible binding of m$^{6}$A reader protein YTHDC1 to its preferred RNA motif. Journal of Chemical Theory and Computation, 15(12):7004-7014.
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Ligand retargeting by binding site analogy. European journal of medicinal chemistry, 175:107-113.
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Unsupervised identification of states from voltage recordings of neural networks. Journal of Neuroscience Methods, 318:104-117.
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Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates. Chemical Reviews, 119(12):6956-6993.
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On the removal of initial state bias from simulation data. Journal of Chemical Physics, 150(10):104105.
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A Reader-Based Assay for mA Writers and Erasers. Analytical Chemistry, 91(4):3078-3084.
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Disulfide bridge formation influences ligand recognition by the ATAD2 bromodomain. Proteins, 87(2):157-167.
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2018
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Protein structure-based drug design: from docking to molecular dynamics. Current Opinion in Structural Biology, 48:93-102.
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Serotonin uptake is required for Rac1 activation in Kras-induced acinar-to-ductal metaplasia in the pancreas. Journal of Pathology, 246(3):352-365.
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In Silico Identification of JMJD3 Demethylase Inhibitors. Journal of Chemical Information and Modeling, 58(10):2151-2163.
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Binding Motifs in the CBP Bromodomain: An Analysis of 20 Crystal Structures of Complexes with Small Molecules. ACS Medicinal Chemistry Letters, 9(9):929-934.
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Structural Analysis of Small-Molecule Binding to the BAZ2A and BAZ2B Bromodomains. ChemMedChem, 13(14):1479-1487.
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Disorder at the Tips of a Disease-Relevant Aβ42 Amyloid Fibril: A Molecular Dynamics Study. Journal of Physical Chemistry B, 122:11072-11082.
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In silico fragment-based drug design with SEED. European journal of medicinal chemistry, 156:907-917.
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Structure-based discovery of selective BRPF1 bromodomain inhibitors. European journal of medicinal chemistry, 155:337-352.
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Iriomoteolides: novel chemical tools to study actin dynamics. Chemical Science, 9(15):3793-3802.
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Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple). ACS Central Science, 4(2):180-188.
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Editorial overview: Folding and binding: In silico, in vitro and in cellula. Current Opinion in Structural Biology, 48:iv-vii.
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2017
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Focused conformational sampling in proteins. Journal of Chemical Physics, 147(19):195102.
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Correction to: The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes. Journal of Biological Chemistry, 292(46):19121.
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Proteomic analyses identify ARH3 as a serine mono-ADP-ribosylhydrolase. Nature Communications, 8(1):2055.
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Discovery of Inhibitors of Four Bromodomains by Fragment-Anchored Ligand Docking. Journal of Chemical Information and Modeling, 57(10):2584-2597.
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Discovery of BAZ2A bromodomain ligands. European journal of medicinal chemistry, 139:564-572.
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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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The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes. Journal of Biological Chemistry, 292(40):16734-16745.
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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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Virtual screen to NMR (VS2NMR): Discovery of fragment hits for the CBP bromodomain. Bioorganic & Medicinal Chemistry Letters, 27(11):2472-2478.
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N,N Dimethylacetamide a drug excipient that acts as bromodomain ligand for osteoporosis treatment. Scientific Reports, 7:42108.
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