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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.
10.1371/journal.pcbi.1005826
http://qmro.qmul.ac.uk/xmlui/handle/123456789/28677
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.
10.1021/acs.jctc.5b00992
http://qmro.qmul.ac.uk/xmlui/handle/123456789/28561
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.
10.1080/07391102.2015.1052016
Lu H-C, Chung SS, Fornili A et al. (2015) . Anatomy of protein disorder, flexibility and disease-related mutations.Front Mol Biosci vol. 2,
10.3389/fmolb.2015.00047
http://qmro.qmul.ac.uk/xmlui/handle/123456789/10431
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.
10.1016/j.bpj.2013.11.253
Carluccio C, Fraternali F, Salvatore F et al. (2013) . Structural features of the regulatory ACT domain of phenylalanine hydroxylase.PLoS ONE vol. 8, (11)
10.1371/journal.pone.0079482
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.
10.1021/ct400486p
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.
10.1093/bioinformatics/btt326
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.
10.1016/j.molcel.2013.04.016
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.
10.1021/ct301118j
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.
10.1586/14789450.2013.856764
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.
10.1096/fj.11-190868
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.
10.1007/978-1-61779-465-0_23
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.
10.1021/ja107640u
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.
10.1016/j.bpj.2010.09.008
Pandini A, Fornili A, Kleinjung J (2010) . Structural alphabets derived from attractors in conformational space.BMC Bioinformatics vol. 11,
10.1186/1471-2105-11-97
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.
10.1021/bi702448s
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.
10.1021/jp0713357
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.
10.1163/157404007782913309
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.
10.1016/j.cplett.2006.06.095
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.
10.1002/jcc.20366
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.
10.1002/jcc.20213
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.
10.1016/j.tetlet.2005.01.108
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.
10.1039/b308248b
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.
10.1016/S0166-1280(03)00296-3
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.
10.1016/S0009-2614(02)01707-4
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.
10.1016/S0957-4166(02)00687-0
FORNILI A (2001) . Water interaction with glycine betaine: A hybrid QM/MM molecular dynamics simulation.Physical Chemistry Chemical Physics vol. 3, 1081-1085.
10.1039/B009779I
Tiberti M, Pandini A, Fraternali F et al.. In silico identification of rescue sites by double force scanning.Bioinformatics
10.1093/bioinformatics/btx515
http://qmro.qmul.ac.uk/xmlui/handle/123456789/25449
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