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Publications:  Dr Arianna Fornili

Rehman S, Grigoryeva LS, Richardson KH, Corsini P, White RC, Shaw R, Portlock TJ, Dorgan B et al.(2020). Structure and functional analysis of the Legionella pneumophila chitinase ChiA reveals a novel mechanism of metal-dependent mucin degradation. PLoS Pathogens vol. 16, (5)
Motta S, Pandini A, Fornili A, Bonati L(2020). Reconstruction of ARNT PAS-B Unfolding Paths by Steered MD and Artificial Neural Network Reveals New Putative Binding Conformations. Biophysical Journal vol. 118, (3) 297A-297A.
Tiberti M, Lechner BD, Fornili A(2019). Binding Pockets in Proteins Induced by Mechanical Stress. Journal of Chemical Theory and Computation vol. 15, (1) 1-6.
Tiberti M, Pandini A, Fraternali F, Fornili A (2018). In Silico Identification of Rescue Sites by Double Force Scanning. BIOPHYSICAL JOURNAL. vol. 114, 43A-43A.
Hashem S, Tiberti M, Fornili A(2017). Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil. PLOS Computational Biology vol. 13, (11) e1005826-e1005826.
Tiberti M, Pandini A, Fraternali F, FORNILI A(2017). In silico identification of rescue sites by double force scanning. Bioinformatics
Pandini A, Fornili A(2016). Using Local States to Drive the Sampling of Global Conformations in Proteins. Journal of Chemical Theory and Computation vol. 12, (3) 1368-1379.
Carluccio C, Fraternali F, Salvatore F, Fornili A, Zagari A(2016). Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylase. Journal of Biomolecular Structure and Dynamics vol. 34, (3) 497-507.
Pandini A, Fornili A (2016). Biasing the Sampling of Local States to Drive the Exploration of Global Conformations in Proteins. BIOPHYSICAL JOURNAL. vol. 110, 187A-188A.
Fornili A, Rostkova E, Fraternali F, Pfuhl M (2016). Effect of RlC N-Terminal Tails on the Structure and Dynamics of Cardiac Myosin. BIOPHYSICAL JOURNAL. vol. 110, 297A-297A.
Lu HC, Chung SS, Fornili A, Fraternali F(2015). Anatomy of protein disorder, flexibility and disease-related mutations. Frontiers in Molecular Biosciences vol. 2, (AUG)
Pandini A, Fornili A, Fraternali F, Kleinjung J (2014). Gsatools: Analysis of Allosteric Communication and Functional Local Motions using a Structural Alphabet. BIOPHYSICAL JOURNAL. vol. 106, 648A-648A.
FORNILI A, Rostkova E, Fraternali F, Pfuhl M(2014). Phosphorylation Modulates the Dynamics of the N-Terminal Tail in Cardiac RLC. Biophysical Journal vol. 106, (2) 33A-33A.
Carluccio C, Fraternali F, Salvatore F, Fornili A, Zagari A(2013). Structural features of the regulatory ACT domain of phenylalanine hydroxylase. PLoS ONE vol. 8, (11)
Fornili A, Pandini A, Lu H-C, Fraternali F(2013). Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles. Journal of Chemical Theory and Computation vol. 9, (11) 5127-5147.
Pandini A, Fornili A, Fraternali F, Kleinjung J(2013). GSATools: Analysis of allosteric communication and functional local motions using a structural alphabet. Bioinformatics vol. 29, (16) 2053-2055.
Vavassori S, Cortini M, Masui S, Sannino S, Anelli T, Caserta IR, Fagioli C, Mossuto MF et al.(2013). A pH-Regulated Quality Control Cycle for Surveillance of Secretory Protein Assembly. Molecular Cell vol. 50, (6) 783-792.
Chakroun N, Fornili A, Prigent S, Kleinjung J, Dreiss CA, Rezaei H, Fraternali F(2013). Decrypting prion protein conversion into a β-rich conformer by molecular dynamics. Journal of Chemical Theory and Computation vol. 9, (5) 2455-2465.
Lu H-C, Fornili A, Fraternali F(2013). Protein-Protein interaction networks studies and importance of 3D structure knowledge. Expert Review of Proteomics vol. 10, (6) 511-520.
Pandini A, Fornili A, Fraternali F, Kleinjung J(2012). Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics. FASEB Journal vol. 26, (2) 868-881.
Pandini A, Fornili A, Fraternali F, Kleinjung J (2012). Detection of Allosteric Signal Transmission by Information-Theoretic Analysis of Protein Dynamics. BIOPHYSICAL JOURNAL. vol. 102, 225A-225A.
Fornili A, Pfuhl M, Fraternali F (2012). Intrinsic Dynamics of the Regulatory Light Chain: Implications on Muscle Contraction. BIOPHYSICAL JOURNAL. vol. 102, 451A-451A.
Fornili A, Autore F, Chakroun N, Martinez P, Fraternali F(2012). Protein-water interactions in MD simulations: POPS/POPSCOMP solvent accessibility analysis, solvation forces and hydration sites. Methods in Molecular Biology vol. 819, 375-392.
Fornili A, Giabbai B, Garau G, Degano M(2010). Energy landscapes associated with macromolecular conformational changes from endpoint structures. Journal of the American Chemical Society vol. 132, (49) 17570-17577.
Autore F, Pagano B, Fornili A, Rittinger K, Fraternali F(2010). In silico phosphorylation of the autoinhibited form of p47phox: Insights into the mechanism of activation. Biophysical Journal vol. 99, (11) 3716-3725.
Pandini A, Fornili A, Kleinjung J(2010). Structural alphabets derived from attractors in conformational space. BMC Bioinformatics vol. 11,
Fornili A, Pandini A, Fraternali F (2010). Interface Dynamics In Hub Proteins. BIOPHYSICAL JOURNAL. vol. 98, 239A-239A.
Iovane E, Giabbai B, Muzzolini L, Matafora V, Fornili A, Minici C, Giannese F, Degano M(2008). Structural basis for substrate specificity in group I nucleoside hydrolases. Biochemistry vol. 47, (15) 4418-4426.
Fornili A, Sironi M, Degano M(2007). Accurate description of nitrogenous base flexibility in classical molecular dynamics simulations of nucleotides bound to proteins. Journal of Physical Chemistry B vol. 111, (23) 6297-6302.
Loos P-F, FORNILI A, Sironi M, Assfeld X(2007). Removing extra frontier parameters in QM/MM methods : a tentative with the Local Self-Consistent Field approach. Computing Letters vol. 3, (2) 473-486.
Fornili A, Loos PF, Sironi M, Assfeld X(2006). Frozen core orbitals as an alternative to specific frontier bond potential in hybrid Quantum Mechanics/Molecular Mechanics methods. Chemical Physics Letters vol. 427, (1-3) 236-240.
Fornili A, Moreau Y, Sironi M, Assfeld X(2006). On the suitability of strictly localized orbitals for hybrid QM/MM calculations. Journal of Computational Chemistry vol. 27, (4) 515-523.
Genoni A, Fornili A, Sironi M(2005). Optimal virtual orbitals to relax wave functions built up with transferred extremely localized molecular orbitals. Journal of Computational Chemistry vol. 26, (8) 827-835.
Morelli CF, Fornili A, Sironi M, Durì L, Speranza G, Manitto P(2005). Evidence for a nucleophilic anti-attack on the cleaved C(2)-oxygen bond in Cl<inf>2</inf>AlH-catalyzed ring-opening of 2-substituted 1,3-dioxolanes. Tetrahedron Letters vol. 46, (11) 1837-1840.
Fornili A, Civera M, Sironi M, Fornili SL(2003). Molecular dynamics simulation of aqueous solutions of trimethylamine-N- oxide and tert-butyl alcohol. Physical Chemistry Chemical Physics vol. 5, (21) 4905-4910.
Fornili A, Sironi M, Raimondi M(2003). Determination of extremely localized molecular orbitals and their application to quantum mechanics/molecular mechanics methods and to the study of intramolecular hydrogen bonding. Journal of Molecular Structure: THEOCHEM vol. 632, (1-3) 157-172.
Civera M, Fornili A, Sironi M, Fornili SL(2003). Molecular dynamics simulation of aqueous solutions of glycine betaine. Chemical Physics Letters vol. 367, (1-2) 238-244.
Morelli CF, Fornili A, Sironi M, Durì L, Speranza G, Manittoa P(2002). Regio- and diastereoselectivity in TiCl<inf>4</inf>-promoted reduction of 2-aryl-substituted cis-4-methyl-5-trifluoromethyl-1,3-dioxolanes. Tetrahedron Asymmetry vol. 13, (23) 2609-2618.
FORNILI A(2001). Water interaction with glycine betaine: A hybrid QM/MM molecular dynamics simulation. Physical Chemistry Chemical Physics vol. 3, 1081-1085.
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