Biblio

Found 32 results
Filters: Author is Caflisch, A. and Keyword is Protein Binding  [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.
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.
2014
Zhao H., Caflisch A..  2014.  Discovery of dual ZAP70 and Syk kinases inhibitors by docking into a rare C-helix-out conformation of Syk. Bioorganic & Medicinal Chemistry Letters. 24(6):1523-1527.
Zhou T., Georgeon S., Moser R., Moore D.J, Caflisch A., Hantschel O..  2014.  Specificity and mechanism-of-action of the JAK2 tyrosine kinase inhibitors ruxolitinib and SAR302503 (TG101348). Leukemia. 28(2):404-407.
2013
Zhao H., Caflisch A..  2013.  Discovery of ZAP70 inhibitors by high-throughput docking into a conformation of its kinase domain generated by molecular dynamics. Bioorganic & Medicinal Chemistry Letters. 23(20):5721-5726.
Steiner S., Magno A., Huang D., Caflisch A..  2013.  Does bromodomain flexibility influence histone recognition? FEBS Letters. 587(14):2158-2163.
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
Steiner S., Caflisch A..  2012.  Peptide binding to the PDZ3 domain by conformational selection. Proteins: Structure, Function, and Bioinformatics. 80(11):2562-2572.
2011
Convertino M., Vitalis A., Caflisch A..  2011.  Disordered binding of small molecules to Aβ(12-28). The Journal of Biological Chemistry. 286(48):41578-41588.
Huang D., Caflisch A..  2011.  The free energy landscape of small molecule unbinding. PLoS Computational Biology. 7(2):e1002002.
Huang D., Caflisch A..  2011.  Small molecule binding to proteins: Affinity and binding/unbinding dynamics from atomistic simulations. ChemMedChem. 6(9):1578-80.
2009
Convertino M., Pellarin R., Catto M., Carotti A., Caflisch A..  2009.  9,10-Anthraquinone hinders beta-aggregation: How does a small molecule interfere with Abeta-peptide amyloid fibrillation? Protein Science. 18(4):792-800.
Ekonomiuk D., Caflisch A..  2009.  Activation of the West Nile virus NS3 protease: Molecular dynamics evidence for a conformational selection mechanism. Protein Science. 18(5):1003-1111.
Exner V., Aichinger E., Shu H., Wildhaber T., Alfarano P., Caflisch A., Gruissem W., Köhler C., Hennig L..  2009.  The chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 is essential for H3K27me3 binding and function during Arabidopsis development. PLoS One. 4(4):e5335.
Ekonomiuk D., Su X.-C., Ozawa K., Bodenreider C., Lim S.P, Yin Z., Keller T.H, Beer D., Patel V., Otting G. et al..  2009.  Discovery of a non-peptidic inhibitor of west nile virus NS3 protease by high-throughput docking. PLoS Neglected Tropical Diseases. 3(1):e356.
Su X.-C., Ozawa K., Yagi H., Lim S.P, Wen D., Ekonomiuk D., Huang D., Keller T.H, Sonntag S., Caflisch A. et al..  2009.  NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease. FEBS Journal. 276(15):4244-4255.
Benedix A., Becker C.M, de Groot B.L, Caflisch A., Böckmann R.A.  2009.  Predicting free energy changes using structural ensembles. Nat Methods. 6(1):3-4.
2008
Interlandi G., Wetzel S.K, Settanni G., Plückthun A., Caflisch A..  2008.  Characterization and further stabilization of designed ankyrin repeat proteins by combining molecular dynamics simulations and experiments. Journal of Molecular Biology. 375(3):837-854.
Kolb P., Huang D., Dey F., Caflisch A..  2008.  Discovery of kinase inhibitors by high-throughput docking and scoring based on a transferable linear interaction energy model. Journal of Medicinal Chemistry. 51(5):1179-1188.
Schenker P., Alfarano P., Kolb P., Caflisch A., Baici A..  2008.  A double-headed cathepsin B inhibitor devoid of warhead. Protein Science. 17(12):2145-2155.
2007
Schroeder V., Vuissoz J.-M., Caflisch A., Kohler H.P.  2007.  Factor XIII activation peptide is released into plasma upon cleavage by thrombin and shows a different structure compared to its bound form. Thrombosis and Haemostasis. 97(6):890-898.
2005
Curcio R., Caflisch A., Paci E..  2005.  Change of the unbinding mechanism upon a mutation: A molecular dynamics study of an antibody-hapten complex. Protein Science. 14(10):2499-2514.
Böckmann R.A, Caflisch A..  2005.  Spontaneous formation of detergent micelles around the outer membrane protein OmpX. Biophysical Journal. 88(5):3191-3204.
2004
Cecchini M., Kolb P., Majeux N., Caflisch A..  2004.  Automated docking of highly flexible ligands by genetic algorithms: A critical assessment. Journal of Computational Chemistry. 25(3):412-422.
Huang D., Caflisch A..  2004.  Efficient evaluation of binding free energy using continuum electrostatics solvation. Journal of Medicinal Chemistry. 47(23):5791-5797.

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