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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)
10.1371/journal.ppat.1008342
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.
10.1016/j.bpj.2019.11.1681
https://qmro.qmul.ac.uk/xmlui/handle/123456789/63431
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.
10.1021/acs.jctc.8b00755
https://qmro.qmul.ac.uk/xmlui/handle/123456789/54640
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.
10.1371/journal.pcbi.1005826
https://qmro.qmul.ac.uk/xmlui/handle/123456789/28677
Tiberti M, Pandini A, Fraternali F, FORNILI A(2017). In silico identification of rescue sites by double force scanning. Bioinformatics
10.1093/bioinformatics/btx515
https://qmro.qmul.ac.uk/xmlui/handle/123456789/25449
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.
10.1021/acs.jctc.5b00992
https://qmro.qmul.ac.uk/xmlui/handle/123456789/28561
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.
10.1080/07391102.2015.1052016
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.
10.1016/j.bpj.2015.11.1045
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.
10.1016/j.bpj.2015.11.1600
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)
10.3389/fmolb.2015.00047
https://qmro.qmul.ac.uk/xmlui/handle/123456789/10431
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.
10.1016/j.bpj.2013.11.3586
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.
10.1016/j.bpj.2013.11.253
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)
10.1371/journal.pone.0079482
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.
10.1021/ct400486p
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.
10.1093/bioinformatics/btt326
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.
10.1016/j.molcel.2013.04.016
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.
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, Kleinjung J(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, Kleinjung J (2012). Detection of Allosteric Signal Transmission by Information-Theoretic Analysis of Protein Dynamics. BIOPHYSICAL JOURNAL. vol. 102, 225A-225A.
10.1016/j.bpj.2011.11.1237
Fornili A, Pfuhl M, Fraternali F (2012). Intrinsic Dynamics of the Regulatory Light Chain: Implications on Muscle Contraction. BIOPHYSICAL JOURNAL. vol. 102, 451A-451A.
10.1016/j.bpj.2011.11.2472
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.
10.1007/978-1-61779-465-0_23
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.
10.1021/ja107640u
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.
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.
10.1016/j.bpj.2009.12.1294
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.
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. Journal of Physical Chemistry B vol. 111, (23) 6297-6302.
10.1021/jp0713357
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.
10.1163/157404007782913309
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.
10.1016/j.cplett.2006.06.095
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.
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. Journal of Computational Chemistry vol. 26, (8) 827-835.
10.1002/jcc.20213
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.
10.1016/j.tetlet.2005.01.108
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.
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, (1-3) 157-172.
10.1016/S0166-1280(03)00296-3
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.
10.1016/S0009-2614(02)01707-4
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.
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
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