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Department of Biochemistry

Publications of Dr. Andreas Vitalis

Cocina, F., Vitalis, A. & Caflisch, A. Spiking burstiness and working memory in the human medial temporal lobe. Cereb Cortex Commun 3, tgac039 (2022). PMID: 36415307.

Ilie, IM., Bacci, M., Vitalis, A. & Caflisch, A. Antibody binding modulates the dynamics of the membrane-bound prion protein. Biophys J 121, 2813-2825 (2022). PMID: 35672948.

Cocina, F., Vitalis, A. & Caflisch, A. Unsupervised Methods for Detection of Neural States: Case Study of Hippocampal-Amygdala Interactions. eNeuro 8, (2021). PMID: 34544761.

Cocina, F., Vitalis, A. & Caflisch, A. Sapphire-Based Clustering. J Chem Theory Comput 16, 6383-6396 (2020). PMID: 32905698.

Marchand, JR., Knehans, T., Caflisch, A. & Vitalis, A. An ABSINTH-Based Protocol for Predicting Binding Affinities between Proteins and Small Molecules. J Chem Inf Model 60, 5188-5202 (2020). PMID: 32897071.

Bacci, M., Caflisch, A. & Vitalis, A. On the removal of initial state bias from simulation data. J Chem Phys 150, 104105 (2019). PMID: 30876362.

Garolini, D., Vitalis, A. & Caflisch, A. Unsupervised identification of states from voltage recordings of neural networks. J Neurosci Methods 318, 104-117 (2019). PMID: 30807781.

Esposito, C. & Vitalis, A. Precise estimation of transfer free energies for ionic species between similar media. Phys Chem Chem Phys 20, 27003-27010 (2018). PMID: 30328430.

Bacci, M., Langini, C., Vymětal, J., Caflisch, A. & Vitalis, A. Focused conformational sampling in proteins. J Chem Phys 147, 195102 (2017). PMID: 29166086.

Bacci, M., Vymětal, J., Mihajlovic, M., Caflisch, A. & Vitalis, A. Amyloid β Fibril Elongation by Monomers Involves Disorder at the Tip. J Chem Theory Comput 13, 5117-5130 (2017). PMID: 28870064.

Langini, C., Caflisch, A. & Vitalis, A. The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes. J Biol Chem 292, 16734-16745 (2017). PMID: 28798233.

Arnon, ZA., Vitalis, A., Levin, A., Michaels, TCT., Caflisch, A., Knowles, TPJ., Adler-Abramovich, L. & Gazit, E. Dynamic microfluidic control of supramolecular peptide self-assembly. Nat Commun 7, 13190 (2016). PMID: 27779182.

Blöchliger, N., Caflisch, A. & Vitalis, A. Weighted Distance Functions Improve Analysis of High-Dimensional Data: Application to Molecular Dynamics Simulations. J Chem Theory Comput 11, 5481-92 (2015). PMID: 26574336.

Bacci, M., Vitalis, A. & Caflisch, A. A molecular simulation protocol to avoid sampling redundancy and discover new states. Biochim Biophys Acta 1850, 889-902 (2015). PMID: 25193737.

Blöchliger, N., Vitalis, A. & Caflisch, A. High-resolution visualisation of the states and pathways sampled in molecular dynamics simulations. Sci Rep 4, 6264 (2014). PMID: 25179558.

Vitalis, A. & Pappu, RV. A simple molecular mechanics integrator in mixed rigid body and dihedral angle space. J Chem Phys 141, 034105 (2014). PMID: 25053299.

Vitalis, A. & Caflisch, A. Equilibrium sampling approach to the interpretation of electron density maps. Structure 22, 156-67 (2014). PMID: 24316403.

Vitalis, A. & Caflisch, A. Efficient Construction of Mesostate Networks from Molecular Dynamics Trajectories. J Chem Theory Comput 8, 1108-20 (2012). PMID: 26593370.

Vitalis, A. & Caflisch, A. 50 Years of Lifson-Roig Models: Application to Molecular Simulation Data. J Chem Theory Comput 8, 363-73 (2012). PMID: 26592894.

Convertino, M., Vitalis, A. & Caflisch, A. Disordered binding of small molecules to Aβ(12-28). J Biol Chem 286, 41578-41588 (2011). PMID: 21969380.

Vitalis, A. & Caflisch, A. Micelle-like architecture of the monomer ensemble of Alzheimer's amyloid-β peptide in aqueous solution and its implications for Aβ aggregation. J Mol Biol 403, 148-165 (2010). PMID: 20709081.