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Institute for Research in Biomedicine
Istituto di Ricerca in Biomedicina

Via Vincenzo Vela 6 - CH-6500 Bellinzona
Tel. +41 91 820 0300 - Fax +41 91 820 0302 - info [at] irb [dot] usi [dot] ch

Andrea Cavalli, PhD

Computational Structural Biology

Group Leader

Via Vela, 6
6500 Bellinzona, Switzerland


Andrea Cavalli earned his degree in theoretical physics at the ETH in Zurich in 1995 and a Ph.D. in mathematics in 2001. After a period in the group of Amedeo Caflisch at the University of Zurich, in 2004 he joined the groups of Christopher Dobson and Michele Vendruscolo at the University of Cambridge, UK, with an Advanced Researcher Fellowship from the Swiss National Science Foundation. During this period of time, his work focused on the development of theoretical and computational methods for the determination of the structure of proteins from sparse experimental data. This line of research led to the development of the CHESHIRE method, which has enabled the first accurate determination of the native state of proteins using NMR chemical shifts (Cavalli et al., Proc Natl Acad Sci USA (2007), vol. 104 (23) pp. 9615-9620) and the structural characterization of the intermediate state of a protein (Neudecker et al., Science (2012), vol. 336(6079), pp. 362-36). In December 2012, he joined the IRB as an Associate Member and was appointed as Group Leader in June 2016. His research is focused on the development of computational methods for the determination of the structure of folded and misfolded states of proteins from minimal sets of experimental data. Andrea Cavalli is also affiliated to the Swiss Institute of Bioinformatics.

Androgen-deprivation therapies for prostate cancer and risk of infection by SARS-CoV-2: a population-based study (N = 4532)
M. Montopoli, S. Zumerle, R. Vettor, M. Rugge, M. Zorzi, C. V. Catapano, G. M. Carbone, A. Cavalli, F. Pagano, E. Ragazzi, T. Prayer-Galetti, A. Alimonti
in Ann Oncol (2020)
How Computational Chemistry and Drug Delivery Techniques Can Support the Development of New Anticancer Drugs
M. Garofalo, G. Grazioso, A. Cavalli, J. Sgrignani
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
A. Marazza, C. Galli, E. Fasana, J. Sgrignani, P. Burda, E. M. A. Fassi, M. Baumgartner, A. Cavalli, M. Molinari
in DNA Cell Biol (2020) vol. 39 pp226-234
Zinc(ii)-mediated diastereoselective Passerini reactions of biocatalytically desymmetrised renewable inputs
L. Moni, L. Banfi, D. Cartagenova, A. Cavalli, C. Lambruschini, E. Martino, R. V. A. Orru, E. Ruijter, J. M. Saya, J. Sgrignani, R. Riva
in Organic Chemistry Frontiers (2020)
Oxidation State Dependent Conformational Changes of HMGB1 Regulate the Formation of the CXCL12/HMGB1 Heterocomplex
E. Fassi, J. Sgrignani, G. D'Agostino, V. Cecchinato, M. Garofalo, G. Grazioso, M. Uguccioni, A. Cavalli
in Computational and Structural Biology Journal (2019) vol. 17 pp886-894
The first‐in‐class ETS inhibitor TK‐216 interferes with ETS transcription factors and synergize with lenalidomide in lymphoma
F. Spriano, E. Chung, S. Napoli, C. Tarantelli, E. Gaudio, L. Cascione, A. Cavalli, A. Rinaldi, I. Kwee, H. Ye, D. Rossi, E. Zucca, A. Stathis, K. Jessen, B. Lannutti, J. Toretsky, F. Bertoni
in Hematological Oncology (2019) vol. 37 pp322
DDR1 role in fibrosis and its pharmacological targeting
S. Moll, A. Desmouliere, M. J. Moeller, J. C. Pache, L. Badi, F. Arcadu, H. Richter, A. Satz, S. Uhles, A. Cavalli, F. Drawnel, L. Scapozza, M. Prunotto
in Biochim Biophys Acta Mol Cell Res (2019) vol. 1866 pp118474
How phosphorylation influences E1 subunit pyruvate dehydrogenase: A computational study
J. Sgrignani, J. Chen, A. Alimonti, A. Cavalli
in Sci Rep (2018) vol. 8 pp14683
Enhancing coevolution-based contact prediction by imposing structural self-consistency of the contacts
M. M. Kassem, L. B. Christoffersen, A. Cavalli, K. Lindorff-Larsen
in Sci Rep (2018) vol. 8 pp11112
Structural Biology of STAT3 and Its Implications for Anticancer Therapies Development
J Sgrignani, M Garofalo, M Matkovic, J Merulla, C. V. Catapano, A. Cavalli
in Int. J. Mol. Sci. (2018) vol. 19 pp1591
Compartmentalized activities of the pyruvate dehydrogenase complex sustain lipogenesis in prostate cancer
J. Chen, I. Guccini, D. D. Mitri, D. Brina, A. Revandkar, M. Sarti, E. Pasquini, A. Alajati, S. Pinton, M. Losa, G. Civenni, C. V. Catapano, J. Sgrignani, A. Cavalli, R. D'Antuono, J. M. Asara, A. Morandi, P. Chiarugi, S. Crotti, M. Agostini, M. Montopoli, I. Masgras, A. Rasola, R. Garcia-Escudero, N. Delaleu, A. Rinaldi, F. Bertoni, J. Bono, A. Carracedo, A. Alimonti
in Nat Genet (2018) vol. 50 pp219-228
A Human Bi-specific Antibody against Zika Virus with High Therapeutic Potential
J. Wang, M. Bardelli, D. A. Espinosa, M. Pedotti, T. S. Ng, S. Bianchi, L. Simonelli, E. X. Y. Lim, M. Foglierini, F. Zatta, S. Jaconi, M. Beltramello, E. Cameroni, G. Fibriansah, J. Shi, T. Barca, I. Pagani, A. Rubio, V. Broccoli, E. Vicenzi, V. Graham, S. Pullan, S. Dowall, R. Hewson, S. Jurt, O. Zerbe, K. Stettler, A. Lanzavecchia, F. Sallusto, A. Cavalli, E. Harris, S. M. Lok, L. Varani, D. Corti
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
A. Magistrato, J. Sgrignani, R. Krause, A. Cavalli
in J Phys Chem Lett (2017) vol. 8 pp2036-2042
The Dynamic Basis for Signal Propagation in Human Pin1-WW
S. Olsson, D. Strotz, B. Vogeli, R. Riek, A. Cavalli
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
J. Sgrignani, A. Cavalli, G. Colombo, A. Magistrato
in Mini Rev Med Chem (2016) vol. 16 pp1112-24
Metainference: A Bayesian inference method for heterogeneous systems
M. Bonomi, C. Camilloni, A. Cavalli, M. Vendruscolo
in Science Advances (2016) vol. 2 pp e1501177
Molecular Determinants for Unphosphorylated STAT3 Dimerization Determined by Integrative Modeling
J. Sgrignani, S. Olsson, D. Ekonomiuk, D. Genini, R. Krause, C. V. Catapano, A. Cavalli
in Biochemistry (2015) vol. 54 pp5489-501
Quantification of Entropy-Loss in Replica-Averaged Modeling
S. Olsson, A. Cavalli
in J Chem Theory Comput (2015) vol. 11 pp3973-7
Dynamic binding mode of a Synaptotagmin-1-SNARE complex in solution
K. D. Brewer, T. Bacaj, A. Cavalli, C. Camilloni, J. D. Swarbrick, J. Liu, A. Zhou, P. Zhou, N. Barlow, J. Xu, A. B. Seven, E. A. Prinslow, R. Voleti, D. Haussinger, A. M. Bonvin, D. R. Tomchick, M. Vendruscolo, B. Graham, T. C. Sudhof, J. Rizo
in Nat Struct Mol Biol (2015) vol. 22 pp555-64
Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3
A. * Cavalli, M. Vendruscolo
in J Biomol NMR (2015) vol. 62 pp503-9
* Co-corresponding author
Molecular Dynamics of Biomolecules through Direct Analysis of Dipolar Couplings
S. Olsson, D. Ekonomiuk, J. Sgrignani, A. Cavalli
in J Am Chem Soc (2015) vol. 137 pp6270-8
Insights into the coiled-coil organization of the Hendra virus phosphoprotein from combined biochemical and SAXS studies
M. Beltrandi, D. Blocquel, J. Erales, P. Barbier, A. * Cavalli, S. Longhi
in Virology (2015) vol. 477 pp42-55
* Co-corresponding author
Characterization of the Conformational Fluctuations in the Josephin Domain of Ataxin-3
D. Sanfelice, A. De Simone, A. Cavalli, S. Faggiano, M. Vendruscolo, A. Pastore
in Biophys J (2014) vol. 107 pp2923-2931
A probabilistic approach to the determination of native state ensembles of proteins
S. Olsson, B.R. Vögeli, A. Cavalli, W. Boomsma, J. Ferkinghoff-Borg, K. Lindorff-Larsen, T. Hamelryck
in J. Chem. Theory Comput. (2014) vol. 10 pp3484-3491
Archaeal MBF1 binds to 30S and 70S ribosomes via its helix-turn-helix domain
F. Blombach, H. Launay, A. P. Snijders, V. Zorraquino, H. Wu, B. de Koning, S. J. Brouns, T. Ettema, C. Camilloni, A. Cavalli, M. Vendruscolo, M. J. Dickman, L. D. Cabrita, A. La Teana, D. Benelli, P. Londei, J. Christodoulou, J. van der Oost
in Biochem J (2014)
ALMOST: An all atom molecular simulation toolkit for protein structure determination
B. Fu, A. B. Sahakyan, C. Camilloni, G. G. Tartaglia, E. Paci, A. Caflisch, M. Vendruscolo, A. Cavalli
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
P. Kukic, C. Camilloni, A. Cavalli, M. Vendruscolo
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
A. Kannan, C. Camilloni, A. B. Sahakyan, A. Cavalli, M. Vendruscolo
in J Am Chem Soc (2014) vol. 136 pp2204-7
Replica-Averaged Metadynamics
C. Camilloni, A. Cavalli, M. Vendruscolo
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
A. Cavalli, C. Camilloni, M. Vendruscolo
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
C. Camilloni, A. Cavalli, M. Vendruscolo
in J Phys Chem B (2013) vol. 117 pp1838-43
Blind testing of routine, fully automated determination of protein structures from NMR data
A. Rosato, J. M. Aramini, C. Arrowsmith, A. Bagaria, D. Baker, A. Cavalli, J. F. Doreleijers, A. Eletsky, A. Giachetti, P. Guerry, A. Gutmanas, P. Guntert, Y. He, T. Herrmann, Y. J. Huang, V. Jaravine, H. R. Jonker, M. A. Kennedy, O. F. Lange, G. Liu, T. E. Malliavin, R. Mani, B. Mao, G. T. Montelione, M. Nilges, P. Rossi, G. van der Schot, H. Schwalbe, T. A. Szyperski, M. Vendruscolo, R. Vernon, W. F. Vranken, Sd Vries, G. W. Vuister, B. Wu, Y. Yang, A. M. Bonvin
in Structure (2012) vol. 20 pp227-36
Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts
C. Camilloni, P. Robustelli, A. De Simone, A. Cavalli, M. Vendruscolo
in J Am Chem Soc (2012) vol. 134 pp3968-71
MYD88 somatic mutations in MALT lymphomas
Z. M. Li, A. Rinaldi, A. Cavalli, A. A. Mensah, M. Ponzoni, R. D. Gascoyne, G. Bhagat, E. Zucca, F. Bertoni
in Br J Haematol (2012) vol. 158 pp662-4
Protein Structure Validation Using Side-Chain Chemical Shifts
A. B. Sahakyan, A. Cavalli, W. F. Vranken, M. Vendruscolo
in J Phys Chem B (2012)
Structure of an intermediate state in protein folding and aggregation
P. Neudecker, P. Robustelli, A. Cavalli, P. Walsh, P. Lundstrom, A. Zarrine-Afsar, S. Sharpe, M. Vendruscolo, L. E. Kay
in Science (2012) vol. 336 pp362-6
Structure-based prediction of methyl chemical shifts in proteins
A. B. Sahakyan, W. F. Vranken, A. Cavalli, M. Vendruscolo
in J Biomol NMR (2011) vol. 50 pp331-46
Using chemical shifts to determine structural changes in proteins upon complex formation
A. Cavalli, R. W. Montalvao, M. Vendruscolo
in J Phys Chem B (2011) vol. 115 pp9491-4
Using side-chain aromatic proton chemical shifts for a quantitative analysis of protein structures
A. B. Sahakyan, W. F. Vranken, A. Cavalli, M. Vendruscolo
in Angew Chem Int Ed Engl (2011) vol. 50 pp9620-3
Insights into protein-protein and enzyme-substrate interactions in modular polyketide synthases
L. Tran, R. W. Broadhurst, M. Tosin, A. Cavalli, K. J. Weissman
in Chem Biol (2010) vol. 17 pp705-16
Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins
P. Robustelli, K. Kohlhoff, A. Cavalli, M. Vendruscolo
in Structure (2010) vol. 18 pp923-33
Accurate random coil chemical shifts from an analysis of loop regions in native states of proteins
A. De Simone, A. Cavalli, S. T. Hsu, W. Vranken, M. Vendruscolo
in J Am Chem Soc (2009) vol. 131 pp16332-3
CASD-NMR: critical assessment of automated structure determination by NMR
A. Rosato, A. Bagaria, D. Baker, B. Bardiaux, A. Cavalli, J. F. Doreleijers, A. Giachetti, P. Guerry, P. Guntert, T. Herrmann, Y. J. Huang, H. R. Jonker, B. Mao, T. E. Malliavin, G. T. Montelione, M. Nilges, S. Raman, G. van der Schot, W. F. Vranken, G. W. Vuister, A. M. Bonvin
in Nat Methods (2009) vol. 6 pp625-6
Fast and accurate predictions of protein NMR chemical shifts from interatomic distances
K. J. Kohlhoff, P. Robustelli, A. Cavalli, X. Salvatella, M. Vendruscolo
in J Am Chem Soc (2009) vol. 131 pp13894-5
Folding of small proteins by Monte Carlo simulations with chemical shift restraints without the use of molecular fragment replacement or structural homology
P. Robustelli, A. Cavalli, C. M. Dobson, M. Vendruscolo, X. Salvatella
in J Phys Chem B (2009) vol. 113 pp7890-6
A coupled equilibrium shift mechanism in calmodulin-mediated signal transduction
J. Gsponer, J. Christodoulou, A. Cavalli, J. M. Bui, B. Richter, C. M. Dobson, M. Vendruscolo
in Structure (2008) vol. 16 pp736-46
Determination of protein structures in the solid state from NMR chemical shifts
P. Robustelli, A. Cavalli, M. Vendruscolo
in Structure (2008) vol. 16 pp1764-9
Identification of aggregation-prone elements by using interaction-energy matrices
J. M. Bui, A. Cavalli, J. Gsponer
in Angew Chem Int Ed Engl (2008) vol. 47 pp7267-9
Structure determination of protein-protein complexes using NMR chemical shifts: case of an endonuclease colicin-immunity protein complex
R. W. Montalvao, A. Cavalli, X. Salvatella, T. L. Blundell, M. Vendruscolo
in J Am Chem Soc (2008) vol. 130 pp15990-6
Prediction of local structural stabilities of proteins from their amino acid sequences
G. G. Tartaglia, A. Cavalli, M. Vendruscolo
in Structure (2007) vol. 15 pp139-43
Protein structure determination from NMR chemical shifts
A. Cavalli, X. Salvatella, C. M. Dobson, M. Vendruscolo
in Proc Natl Acad Sci U S A (2007) vol. 104 pp9615-20
Geometry, energetics, and dynamics of hydrogen bonds in proteins: structural information derived from NMR scalar couplings
J. Gsponer, H. Hopearuoho, A. Cavalli, C. M. Dobson, M. Vendruscolo
in J Am Chem Soc (2006) vol. 128 pp15127-35
Comparison of sequence-based and structure-based energy functions for the reversible folding of a peptide
A. Cavalli, M. Vendruscolo, E. Paci
in Biophys J (2005) vol. 88 pp3158-66
Organism complexity anti-correlates with proteomic beta-aggregation propensity
G. G. Tartaglia, R. Pellarin, A. Cavalli, A. Caflisch
in Protein Sci (2005) vol. 14 pp2735-40
Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences
G. G. Tartaglia, A. Cavalli, R. Pellarin, A. Caflisch
in Protein Sci (2005) vol. 14 pp2723-34
The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates
G. G. Tartaglia, A. Cavalli, R. Pellarin, A. Caflisch
in Protein Sci (2004) vol. 13 pp1939-41
Analysis of the distributed computing approach applied to the folding of a small beta peptide
E. Paci, A. Cavalli, M. Vendruscolo, A. Caflisch
in Proc Natl Acad Sci U S A (2003) vol. 100 pp8217-22
Fast protein folding on downhill energy landscape
A. Cavalli, U. Haberthur, E. Paci, A. Caflisch
in Protein Sci (2003) vol. 12 pp1801-3
Weak temperature dependence of the free energy surface and folding pathways of structured peptides
A. Cavalli, P. Ferrara, A. Caflisch
in Proteins (2002) vol. 47 pp305-14