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Publications:  Dr Arianna Fornili

Hashem S, Tiberti M, Fornili A(2017). Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil. PLOS Computational Biology vol. 13, (11) e1005826-e1005826.
Pandini A, Fornili A(2016). Using Local States To Drive the Sampling of Global Conformations in Proteins. J Chem Theory Comput vol. 12, (3) 1368-1379.
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 et al. (2016). Effect of RlC N-Terminal Tails on the Structure and Dynamics of Cardiac Myosin. BIOPHYSICAL JOURNAL. vol. 110, 297A-297A.
Carluccio C, Fraternali F, Salvatore F et al.(2016). Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylase. J Biomol Struct Dyn vol. 34, (3) 497-507.
Lu H-C, Chung SS, Fornili A et al.(2015). Anatomy of protein disorder, flexibility and disease-related mutations. Front Mol Biosci vol. 2,
Pandini A, Fornili A, Fraternali F et al. (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 et al.(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 et al.(2013). Structural features of the regulatory ACT domain of phenylalanine hydroxylase. PLoS ONE vol. 8, (11)
Fornili A, Pandini A, Lu H-C et al.(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 et al.(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 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 et al.(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 et al.(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 et al. (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 et al.(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 et al.(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 et al.(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 et al.(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. J Phys Chem B vol. 111, (23) 6297-6302.
Loos P-F, FORNILI A, Sironi M et al.(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 et al.(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 et al.(2006). On the suitability of strictly localized orbitals for hybrid QM/MM calculations. J Comput Chem 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. J Comput Chem vol. 26, (8) 827-835.
Morelli CF, Fornili A, Sironi M et al.(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 et al.(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, 157-172.
Civera M, Fornili A, Sironi M et al.(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 et al.(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.
Tiberti M, Pandini A, Fraternali F et al.(2017). In silico identification of rescue sites by double force scanning. Bioinformatics
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