Biblio

Found 31 results
Filters: Author is Caflisch, A. and Keyword is Molecular Dynamics Simulation  [Clear All Filters]
2023
Xiang Y., Zhai G., Li Y., Wang M., Chen X., Wang R., Xie H., Zhang W., Ge G., Zhang Q. et al..  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
Dehabadi M.H, Caflisch A., Ilie I.M, Firouzi R..  2022.  Interactions of curcumin's degradation products with the Aβ dimer: a computational study. The Journal of Physical Chemistry B. 126(39):7627-7637.
2017
Langini C., Caflisch A., Vitalis A..  2017.  The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes. The Journal of Biological Chemistry. 292(40):16734-16745.
2016
Reichen C., Hansen S., Forzani C., Honegger A., Fleishman S.J, Zhou T., Parmeggiani F., Ernst P., Madhurantakam C., Ewald C. et al..  2016.  Computationally designed armadillo repeat proteins for modular peptide recognition. Journal of Molecular Biology. 428(22):4467-4489.
Müller C.S, Knehans T., Davydov D.R, Bounds P.L, von Mandach U., Halpert J.R, Caflisch A., Koppenol W.H.  2016.  Correction to "Concurrent cooperativity and substrate inhibition in the epoxidation of carbamazepine by cytochrome P450 3A4 active site mutants inspired by molecular dynamics simulations". Biochemistry. 55(39):5647.
Xu M., Caflisch A., Hamm P..  2016.  Protein structural memory influences ligand binding mode(s) and unbinding rates. Journal of Chemical Theory and Computation. 12(3):1393-1399.
Ben Halima S., Mishra S., Raja K.MP, Willem M., Baici A., Simons K., Brüstle O., Koch P., Haass C., Caflisch A. et al..  2016.  Specific inhibition of β-secretase processing of the Alzheimer disease amyloid precursor protein. Cell Reports. 14(9):2127-2141.
2015
Müller C.S, Knehans T., Davydov D.R, Bounds P.L, von Mandach U., Halpert J.R, Caflisch A., Koppenol W.H.  2015.  Concurrent cooperativity and substrate inhibition in the epoxidation of carbamazepine by cytochrome P450 3A4 active site mutants inspired by molecular dynamics simulations. Biochemistry. 54(3):711-721.
Huang D., Caflisch A..  2015.  The roles of the conserved tyrosine in the β2-α2 loop of the prion protein. Prion. 9(6):412-419.
2014
Fu B., Sahakyan A.B, Camilloni C., Tartaglia G.G, Paci E., Caflisch A., Vendruscolo M., Cavalli A..  2014.  ALMOST: An all atom molecular simulation toolkit for protein structure determination. Journal of Computational Chemistry. 35(14):1101-1105.
Huang D., Rossini E., Steiner S., Caflisch A..  2014.  Structured water molecules in the binding site of bromodomains can be displaced by cosolvent. ChemMedChem. 9(3):573-579.
Friedman R., Caflisch A..  2014.  Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends: A simulation study. Proteins: Structure, Function, and Bioinformatics. 82(3):399-404.
2013
Attanasio F., Convertino M., Magno A., Caflisch A., Corazza A., Haridas H., Esposito G., Cataldo S., Pignataro B., Milardi D. et al..  2013.  Carnosine inhibits Aβ42 aggregation by perturbing the H-bond network in and around the central hydrophobic cluster. ChemBioChem. 14(5):583-592.
Steiner S., Magno A., Huang D., Caflisch A..  2013.  Does bromodomain flexibility influence histone recognition? FEBS Letters. 587(14):2158-2163.
Buchli B., Waldauer S.A, Walser R., Donten M.L, Pfister R., Blöchliger N., Steiner S., Caflisch A., Zerbe O., Hamm P..  2013.  Kinetic response of a photoperturbed allosteric protein. Proceedings of the National Academy of Sciences of the United States of America. 110(29):11725-11730.
Scherzer-Attali R., Convertino M., Pellarin R., Gazit E., Segal D., Caflisch A..  2013.  Methylations of tryptophan-modified naphthoquinone affect its inhibitory potential toward Aβ aggregation. The Journal of Physical Chemistry B. 117(6):1780-1789.
Kalgin I.V, Caflisch A., Chekmarev S.F, Karplus M..  2013.  New insights into the folding of a β-sheet miniprotein in a reduced space of collective hydrogen bond variables: Application to a hydrodynamic analysis of the folding flow. The Journal of Physical Chemistry B. 117(20):6092-6105.
Lafleur K., Dong J., Huang D., Caflisch A., Nevado C..  2013.  Optimization of inhibitors of the tyrosine kinase EphB4. 2. Cellular potency improvement and binding mode validation by X-ray crystallography. Journal of Medicinal Chemistry. 56(1):84-96.
2012
Zhao H., Huang D., Caflisch A..  2012.  Discovery of tyrosine kinase inhibitors by docking into an inactive kinase conformation generated by molecular dynamics. ChemMedChem. 7(11):1983-1990.
Rennebaum S., Caflisch A..  2012.  Inhibition of interdomain motion in g-actin by the natural product latrunculin: A molecular dynamics study. Proteins: Structure, Function, and Bioinformatics. 80(8):1998-2008.
Alfarano P., Varadamsetty G., Ewald C., Parmeggiani F., Pellarin R., Zerbe O., Plückthun A., Caflisch A..  2012.  Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy. Protein Science. 21(9):1298-1314.
Steiner S., Caflisch A..  2012.  Peptide binding to the PDZ3 domain by conformational selection. Proteins: Structure, Function, and Bioinformatics. 80(11):2562-2572.
Waldauer S.A, Hassan S., Paoli B., Donaldson P.M, Pfister R., Hamm P., Caflisch A., Pellarin R..  2012.  Photocontrol of reversible amyloid formation with a minimal-design peptide. The Journal of Physical Chemistry B. 116(30):8961-8973.
2011
Mishra S., Caflisch A..  2011.  Dynamics in the active site of β-secretase: A network analysis of atomistic simulations. Biochemistry. 50(43):9328-9339.
Scalco R., Caflisch A..  2011.  Equilibrium distribution from distributed computing (simulations of protein folding). The Journal of Physical Chemistry B. 115(19):6358-6365.

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