Cavalli Andrea, PhD

Publications -> 20782

• Androgen-deprivation therapies for prostate cancer and risk of infection by SARS-CoV-2: a population-based study (N = 4532)
  Montopoli, M. Zumerle, S. Vettor, R. Rugge, M. Zorzi, M. Catapano, C. V. Carbone, G. M. Cavalli, A. Pagano, F. Ragazzi, E. Prayer-Galetti, T. Alimonti, A.
  in Ann Oncol (2020) Vol. pp
  
• How Computational Chemistry and Drug Delivery Techniques Can Support the Development of New Anticancer Drugs
  Garofalo, M. Grazioso, G. Cavalli, A.
  in Molecules (2020) Vol.25 pppii: E1756
  
• Endoplasmic Reticulum and Lysosomal Quality Control of Four Nonsense Mutants of Iduronate 2-Sulfatase Linked to Hunter’s Syndrome
  Marazza, A. Galli, C. Fasana, E. Burda, P. Fassi, E. M. A. Baumgartner, M. Cavalli, A. Molinari, M.
  in DNA Cell Biol (2020) Vol.39 pp226-234
  
• Zinc(ii)-mediated diastereoselective Passerini reactions of biocatalytically desymmetrised renewable inputs
  Moni, L. Banfi, L. Cartagenova, D. Lambruschini, C. Martino, E. Orru, R. V. A. Ruijter, E. Saya, J. M. Sgrignani, J. Riva, R.
  in Organic Chemistry Frontiers (2019) Vol. pp
  
• Oxidation State Dependent Conformational Changes of HMGB1 Regulate the Formation of the CXCL12/HMGB1 Heterocomplex
  Fassi, E. M. A. Sgrignani, J. D'Agostino, G. Garofalo, M. Grazioso, G. Uguccioni, M. Cavalli, A.
  in Comput Struct Biotechnol J (2019) Vol.17 pp886-894
  
• The first‐in‐class ETS inhibitor TK‐216 interferes with ETS transcription factors and synergize with lenalidomide in lymphoma
  Spriano, F. Chung,E. Napoli, S. Gaudio, E. Cascione, L. Cavalli, A. Rinaldi, A. Kwee, I. Ye, H. Rossi, D. Zucca, E. Stathis, A. Jessen, K. Lannutti, B. Toretsky, J. Bertoni, F.
  in Hematological Oncology (2019) Vol.37 pp322
  
• DDR1 role in fibrosis and its pharmacological targeting
  Moll, S. Desmouliere, A. Moeller, M. J. Badi, L. Arcadu, F. Richter, H. Satz, A. Uhles, S. Cavalli, A. Drawnel, F. Scapozza, L. Prunotto, M.
  in Biochim Biophys Acta Mol Cell Res (2019) Vol.1866 pp118474
  
• How phosphorylation influences E1 subunit pyruvate dehydrogenase: A computational study
  Sgrignani, J. Chen, J. Alimonti, A.
  in Sci Rep (2018) Vol.8 pp14683
  
• Enhancing coevolution-based contact prediction by imposing structural self-consistency of the contacts
  Kassem, M. M. Christoffersen, L. B. Cavalli, A.
  in Sci Rep (2018) Vol.8 pp11112
  
• Structural Biology of STAT3 and Its Implications for Anticancer Therapies Development
  Sgrignani, J Garofalo, M Matkovic, M Catapano, C. V. Cavalli, A.
  in Int. J. Mol. Sci. (2018) Vol.19 pp1591
  
• A Human Bi-specific Antibody against Zika Virus with High Therapeutic Potential
  Wang, J. Bardelli, M. Espinosa, D. A. Ng, T. S. Bianchi, S. Simonelli, L. Lim, E. X. Y. Foglierini, M. Zatta, F. Jaconi, S. Beltramello, M. Cameroni, E. Fibriansah, G. Shi, J. Barca, T. Pagani, I. Rubio, A. Broccoli, V. Vicenzi, E. Graham, V. Pullan, S. Dowall, S. Hewson, R. Jurt, S.Zerbe, O. Stettler, K. Lanzavecchia, A. Sallusto, F. Cavalli, A.
  in Cell (2017) Vol.171 pp229-241 e15
  * J. Wang and M. Bardelli contributed equally ; S-M Lok, L.Varani and D. Corti contributed equally.
• Single or Multiple Access Channels to the CYP450s Active Site? an Answer from Free Energy Simulations of the Human Aromatase Enzyme
  Magistrato, A. Sgrignani, J. Krause, R.
  in J Phys Chem Lett (2017) Vol.8 pp2036-2042
  
• The Dynamic Basis for Signal Propagation in Human Pin1-WW
  Olsson, S. Strotz, D. Vogeli, B. Cavalli, A.
  in Structure (2016) Vol.24 pp1464-75
  S. Olsson and A. Cavalli are co-corresponding authors.
• Enzymatic and Inhibition Mechanism of Human Aromatase (CYP19A1) Enzyme. A Computational Perspective from QM/MM and Classical Molecular Dynamics Simulations
  Sgrignani, J. Cavalli, A. Colombo, G.
  in Mini Rev Med Chem (2016) Vol.16 pp1112-24
  
• Metainference: A Bayesian inference method for heterogeneous systems
  Bonomi, M. Camilloni, C. Cavalli, A.
  in Science Advances (2016) Vol.2 ppe1501177
  
• Molecular Determinants for Unphosphorylated STAT3 Dimerization Determined by Integrative Modeling
  Sgrignani, J. Olsson, S. Ekonomiuk, D. Krause, R. Catapano, C. V. Cavalli, A.
  in Biochemistry (2015) Vol.54 pp5489-501
  
• Quantification of Entropy-Loss in Replica-Averaged Modeling
  Olsson, S. Cavalli, A.
  in J Chem Theory Comput (2015) Vol.11 pp3973-7
  
• Dynamic binding mode of a Synaptotagmin-1-SNARE complex in solution
  Brewer, K. D. Bacaj, T. Cavalli, A. Swarbrick, J. D. Liu, J. Zhou, A. Zhou, P. Barlow, N. Xu, J. Seven, A. B. Prinslow, E. A. Voleti, R. Haussinger, D. Bonvin, A. M. Tomchick, D. R. Vendruscolo, M. Graham, B. Sudhof, T. C. Rizo, J.
  in Nat Struct Mol Biol (2015) Vol.22 pp555-64
  
• Molecular Dynamics of Biomolecules through Direct Analysis of Dipolar Couplings
  Olsson, S. Ekonomiuk, D. Sgrignani, J.
  in J Am Chem Soc (2015) Vol.137 pp6270-8
  
• Compartmentalized activities of the pyruvate dehydrogenase complex sustain lipogenesis in prostate cancer
  Chen, J. Guccini, I. Mitri, D. D. Revandkar, A. Sarti, M. Pasquini, E. Alajati, A. Pinton, S. Losa, M. Civenni, G. Catapano, C. V. Sgrignani, J. Cavalli, A. D'Antuono, R. Asara, J. M. Morandi, A. Chiarugi, P. Crotti, S. Agostini, M. Montopoli, M. Masgras, I. Rasola, A. Garcia-Escudero, R. Delaleu, N. Rinaldi, A. Bertoni, F. Bono, J. Carracedo, A. Alimonti, A.
  in Nat Genet (2015) Vol.50 pp219-228
  
• Characterization of the Conformational Fluctuations in the Josephin Domain of Ataxin-3
  Sanfelice, D. De Simone, A. Cavalli, A. Vendruscolo, M. Pastore, A.
  in Biophys J (2014) Vol.107 pp2923-2931
  
• A probabilistic approach to the determination of native state ensembles of proteins
  Olsson, S. Vögeli, B.R. Cavalli, A. Ferkinghoff-Borg, J. Lindorff-Larsen, K. Hamelryck, T.
  in J. Chem. Theory Comput. (2014) Vol.10 pp3484-3491
  
• Archaeal MBF1 binds to 30S and 70S ribosomes via its helix-turn-helix domain
  Blombach, F. Launay, H. Snijders, A. P. Wu, H. de Koning, B. Brouns, S. J. Ettema, T. Camilloni, C. Cavalli, A. Vendruscolo, M. Dickman, M. J. Cabrita, L. D. La Teana, A. Benelli, D. Londei, P. Christodoulou, J. van der Oost, J.
  in Biochem J (2014) Vol. pp
  
• ALMOST: An all atom molecular simulation toolkit for protein structure determination
  Fu, B. Sahakyan, A. B. Camilloni, C. Paci, E. Caflisch, A. Vendruscolo, M. Cavalli, A.
  in J Comput Chem (2014) Vol.35 pp1101-5
  
• Determination of the individual roles of the linker residues in the interdomain motions of calmodulin using NMR chemical shifts
  Kukic, P. Camilloni, C. Cavalli, A.
  in J Mol Biol (2014) Vol.426 pp1826-38
  
• A conformational ensemble derived using NMR methyl chemical shifts reveals a mechanical clamping transition that gates the binding of the HU protein to DNA
  Kannan, A. Camilloni, C. Sahakyan, A. B. Vendruscolo, M.
  in J Am Chem Soc (2013) Vol.136 pp2204-7
  
• Replica-Averaged Metadynamics
  Camilloni, C. Cavalli, A. Vendruscolo, M.
  in J. Chem. Theory Comput. (2013) Vol.12 pp5610-17
  
• Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle
  Cavalli, A. Camilloni, C. Vendruscolo, M.
  in J Chem Phys (2013) Vol.138 pp094112
  
• Assessment of the use of NMR chemical shifts as replica-averaged structural restraints in molecular dynamics simulations to characterize the dynamics of proteins
  Camilloni, C. Cavalli, A. Vendruscolo, M.
  in J Phys Chem B (2013) Vol.117 pp1838-43
  
• MYD88 somatic mutations in MALT lymphomas
  Li, Z. M. Rinaldi, A. Cavalli, A. Ponzoni, M. Gascoyne, R. D. Bhagat, G. Zucca, E. Bertoni, F.
  in Br J Haematol (2012) Vol.158 pp662-4
  
• Structure of an intermediate state in protein folding and aggregation
  Neudecker, P. Robustelli, P. Cavalli, A. Lundstrom, P. Zarrine-Afsar, A. Sharpe, S. Vendruscolo, M. Kay, L. E.
  in Science (2012) Vol.336 pp362-6
  
• Protein Structure Validation Using Side-Chain Chemical Shifts
  Sahakyan, A. B. Cavalli, A. Vranken, W. F.
  in J Phys Chem B (2012) Vol. pp
  
• Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts
  Camilloni, C. Robustelli, P. De Simone, A. Vendruscolo, M.
  in J Am Chem Soc (2012) Vol.134 pp3968-71
  
• Blind testing of routine, fully automated determination of protein structures from NMR data
  Rosato, A. Aramini, J. M. Arrowsmith, C. Baker, D. Cavalli, A. Doreleijers, J. F. Eletsky, A. Giachetti, A. Guerry, P. Gutmanas, A. Guntert, P. He, Y. Herrmann, T. Huang, Y. J. Jaravine, V. Jonker, H. R. Kennedy, M. A. Lange, O. F. Liu, G. Malliavin, T. E. Mani, R. Mao, B. Montelione, G. T. Nilges, M.Rossi, P. van der Schot, G. Schwalbe, H. Szyperski, T. A. Vendruscolo, M.
  in Structure (2012) Vol.20 pp227-36
  
• Using side-chain aromatic proton chemical shifts for a quantitative analysis of protein structures
  Sahakyan, A. B. Vranken, W. F. Cavalli, A.
  in Angew Chem Int Ed Engl (2011) Vol.50 pp9620-3
  
• Using chemical shifts to determine structural changes in proteins upon complex formation
  Cavalli, A. Montalvao, R. W. Vendruscolo, M.
  in J Phys Chem B (2011) Vol.115 pp9491-4
  
• Structure-based prediction of methyl chemical shifts in proteins
  Sahakyan, A. B. Vranken, W. F. Cavalli, A.
  in J Biomol NMR (2011) Vol.50 pp331-46
  
• Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins
  Robustelli, P. Kohlhoff, K. Cavalli, A.
  in Structure (2010) Vol.18 pp923-33
  
• Insights into protein-protein and enzyme-substrate interactions in modular polyketide synthases
  Tran, L. Broadhurst, R. W. Tosin, M. Weissman, K. J.
  in Chem Biol (2010) Vol.17 pp705-16
  
• Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins
  De Simone, A. Cavalli, A. Hsu, S. T. Vendruscolo, M.
  in J Am Chem Soc (2009) Vol.131 pp16332-3
  
• Fast and accurate predictions of protein NMR chemical shifts from interatomic distances
  Kohlhoff, K. J. Robustelli, P. Cavalli, A. Vendruscolo, M.
  in J Am Chem Soc (2009) Vol.131 pp13894-5
  
• CASD-NMR: critical assessment of automated structure determination by NMR
  Rosato, A. Bagaria, A. Baker, D. Cavalli, A. Doreleijers, J. F. Giachetti, A. Guerry, P. Guntert, P. Herrmann, T. Huang, Y. J. Jonker, H. R. Mao, B. Malliavin, T. E. Montelione, G. T. Nilges, M. Raman, S. van der Schot, G. Vranken, W. F. Vuister, G. W. Bonvin, A. M.
  in Nat Methods (2009) Vol.6 pp625-6
  
• Folding of small proteins by Monte Carlo simulations with chemical shift restraints without the use of molecular fragment replacement or structural homology
  Robustelli, P. Cavalli, A. Dobson, C. M. Salvatella, X.
  in J Phys Chem B (2009) Vol.113 pp7890-6
  
• Determination of protein structures in the solid state from NMR chemical shifts
  Robustelli, P. Cavalli, A. Vendruscolo, M.
  in Structure (2008) Vol.16 pp1764-9
  
• Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex
  Montalvao, R. W. Cavalli, A. Salvatella, X. Vendruscolo, M.
  in J Am Chem Soc (2008) Vol.130 pp15990-6
  
• Identification of aggregation-prone elements by using interaction-energy matrices
  Bui, J. M. Cavalli, A. Gsponer, J.
  in Angew Chem Int Ed Engl (2008) Vol.47 pp7267-9
  
• A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction
  Gsponer, J. Christodoulou, J. Cavalli, A. Richter, B. Dobson, C. M. Vendruscolo, M.
  in Structure (2008) Vol.16 pp736-46
  
• Protein structure determination from NMR chemical shifts
  Cavalli, A. Salvatella, X. Dobson, C. M.
  in Proc Natl Acad Sci U S A (2007) Vol.104 pp9615-20
  
• Prediction of local structural stabilities of proteins from their amino acid sequences
  Tartaglia, G. G. Cavalli, A. Vendruscolo, M.
  in Structure (2007) Vol.15 pp139-43
  
• Geometry, energetics, and dynamics of hydrogen bonds in proteins: structural information derived from NMR scalar couplings
  Gsponer, J. Hopearuoho, H. Cavalli, A. Vendruscolo, M.
  in J Am Chem Soc (2006) Vol.128 pp15127-35
  
• Organism complexity anti-correlates with proteomic beta-aggregation propensity
  Tartaglia, G. G. Pellarin, R. Cavalli, A.
  in Protein Sci (2005) Vol.14 pp2735-40
  
• Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences
  Tartaglia, G. G. Cavalli, A. Pellarin, R.
  in Protein Sci (2005) Vol.14 pp2723-34
  
• Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide
  Cavalli, A. Vendruscolo, M. Paci, E.
  in Biophys J (2005) Vol.88 pp3158-66
  
• The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates
  Tartaglia, G. G. Cavalli, A. Pellarin, R.
  in Protein Sci (2004) Vol.13 pp1939-41
  
• Fast protein folding on downhill energy landscape
  Cavalli, A. Haberthur, U. Paci, E.
  in Protein Sci (2003) Vol.12 pp1801-3
  
• Analysis of the distributed computing approach applied to the folding of a small beta peptide
  Paci, E. Cavalli, A. Vendruscolo, M.
  in Proc Natl Acad Sci U S A (2003) Vol.100 pp8217-22
  
• Weak temperature dependence of the free energy surface and folding pathways of structured peptides
  Cavalli, A. Ferrara, P. Caflisch, A.
  in Proteins (2002) Vol.47 pp305-14