Biblio
Found 28 results
Filters: Author is Caflisch, A. and Keyword is Proteins [Clear All Filters]
Derivatives of 3-amino-2-methylpyridine as BAZ2B bromodomain ligands: In silico discovery and in crystallo validation. Journal of Medicinal Chemistry. 59(21):9919-9927.
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2016. The "gatekeeper" residue influences the mode of binding of acetyl indoles to bromodomains. Journal of Medicinal Chemistry. 59(7):3087-3097.
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2016. High-throughput fragment docking into the BAZ2B bromodomain: Efficient in silico screening for X-Ray crystallography. ACS Chemical Biology. 11(3):800-807.
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2016. ALMOST: An all atom molecular simulation toolkit for protein structure determination. Journal of Computational Chemistry. 35(14):1101-1105.
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2014. 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.
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2013. Equilibrium distribution from distributed computing (simulations of protein folding). The Journal of Physical Chemistry B. 115(19):6358-6365.
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2011. Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. Journal of Computational Chemistry. 32(6):1183-1194.
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2011. CHARMM: The biomolecular simulation program. Journal of Computational Chemistry. 30(10):1545-1614.
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2009. Identification of the protein folding transition state from molecular dynamics trajectories. Journal of Chemical Physics. 130(12):125104.
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2009. Predicting free energy changes using structural ensembles. Nat Methods. 6(1):3-4.
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2009. FACTS: Fast analytical continuum treatment of solvation. Journal of Computational Chemistry. 29(5):701-715.
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2008. One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: New insights into the folding process. The Journal of Physical Chemistry B. 112(29):8701-8714.
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2008. Wordom: A program for efficient analysis of molecular dynamics simulations. Bioinformatics. 23(19):2625-2627.
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2007. Automatic and efficient decomposition of two-dimensional structures of small molecules for fragment-based high-throughput docking. Journal of Medicinal Chemistry. 49(25):7384-7392.
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2006. Computational models for the prediction of polypeptide aggregation propensity. Current Opinion in Chemical Biology. 10(5):437-444.
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2006. Estimation of protein folding probability from equilibrium simulations. Journal of Chemical Physics. 122(18):184901.
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2005. Organism complexity anti-correlates with proteomic beta-aggregation propensity. Protein Science. 14(10):2735-2740.
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2005. Spontaneous formation of detergent micelles around the outer membrane protein OmpX. Biophysical Journal. 88(5):3191-3204.
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2005. Protein folding: Simple models for a complex process. Structure. 12(10):1750-1752.
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2004. The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates. Protein Science. 13(7):1939-1941.
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2004. Combining task- and data parallelism to speed up protein folding on a desktop grid platform. Proceedings of the 3rd IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2003).
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2003. Efficient evaluation of the effective dielectric function of a macromolecule in aqueous solution. Journal of Computational Chemistry. 24(15):1936-1949.
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2003. Fast protein folding on downhill energy landscape. Protein Science. 12(8):1801-1803.
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2003. Folding for binding or binding for folding? Trends in Biotechnology. 21(10):423-425.
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2003. A sphere-based model for the electrostatics of globular proteins. Journal of the American Chemical Society. 125(15):4600-4608.
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