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Research

Publications: Dr Arianna Fornili

Fornili A, Hashem S, Davies WG ( 2020 ) . Heart Failure Drug Modifies the Intrinsic Dynamics of the Pre-Power Stroke State of Cardiac Myosin . Journal of Chemical Information and Modeling
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 .
Hashem S, Tiberti M, Fornili A ( 2018 ) . Allosteric Modulation of Cardiac Myosin Dynamics by Omecamtiv Mecarbil . Biophysical Journal . vol. 114 , 36a - 37a .
Tiberti M, Lechner B-D, Fornili A ( 2018 ) . Binding Pockets Under Mechanical Stress . Biophysical Journal . vol. 114 ,
Tiberti M, Pandini A, Fraternali F, Fornili A ( 2018 ) . In Silico Identification of Rescue Sites by Double Force Scanning . Biophysical Journal . vol. 114 ,
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 ,
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 ,
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 ,
Fornili A, Pfuhl M, Fraternali F ( 2012 ) . Intrinsic Dynamics of the Regulatory Light Chain: Implications on Muscle Contraction . Biophysical Journal . vol. 102 ,
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 ,
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 .
Morelli CF, Fornili A, Sironi M, Duri L, Speranza G, Manitto P ( 2005 ) . Evidence for a Nucleophilic anti‐Attack on the Cleaved C(2)‐Oxygen Bond in Cl2‐AlH‐Catalyzed Ring‐Opening of 2‐Substituted 1,3‐Dioxolanes . ChemInform vol. 36 , ( 27 )
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 .
Morelli CF, Fornili A, Sironi M, Duri L, Speranza G, Manittoa P ( 2003 ) . Regio‐ and Diastereoselectivity in TiCl4‐Promoted Reduction of 2‐Aryl‐Substituted cis‐4‐Methyl‐5‐trifluoromethyl‐1,3‐dioxolanes . ChemInform vol. 34 , ( 15 )
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 .