Publications: Dr Arianna Fornili
Matsingos C, Howell LA, McCormick PJ, Fornili A
(
2024
)
.
Elucidating the Activation Mechanism of the Proton-sensing GPR68 Receptor
.
Journal of Molecular Biology
vol.
436
,
(
16
)
Rehman S, Antonovic AK, McIntire IE, Zheng H, Cleaver L, Baczynska M, Adams CO, Portlock T et al.
(
2024
)
.
The Legionella collagen-like protein employs a distinct binding mechanism for the recognition of host glycosaminoglycans
.
Nature Communications
vol.
15
,
(
1
)
Kliza KW, Song W, Pinzuti I, Schaubeck S, Kunzelmann S, Kuntin D, Fornili A, Pandini A et al.
(
2024
)
.
N4BP1 functions as a dimerization-dependent linear ubiquitin reader which regulates TNF signalling
.
Cell Death Discovery
vol.
10
,
(
1
)
Rehman S, Antonovic AK, McIntire IE, Zheng H, Cleaver L, Adams CO, Portlock T, Richardson K et al.
(
2023
)
.
The Legionella collagen-like protein employs a unique binding mechanism for the recognition of host glycosaminoglycans
.
vol.
4
,
(
12-15
)
Sonne A, Antonovic AK, Melhedegaard E, Akter F, Andersen JL, Jungbluth H, Witting N, Vissing J et al.
(
2023
)
.
Abnormal myosin post‐translational modifications and ATP turnover time associated with human congenital myopathy‐related RYR1 mutations
.
Acta Physiologica
vol.
239
,
(
2
)
Akter F, Ochala J, Fornili A
(
2023
)
.
Binding pocket dynamics along the recovery stroke of human β-cardiac myosin
.
PLOS Computational Biology
vol.
19
,
(
5
)
Antonovic AK, Ochala J, Fornili A
(
2023
)
.
A rational approach to selective targeting of skeletal myosin
.
Biophysical Journal
vol.
122
,
(
3
)
Antonovic AK, Ochala J, Fornili A
(
2022
)
.
Comparative study of binding pocket structure and dynamics in cardiac and skeletal myosin
.
Biophysical Journal
vol.
122
,
(
1
)
54
-
62
.
Colomba A, Claus J, Gao F, George R, Fornili A, Cameron AJM
(
2022
)
.
Targeting the HER3 pseudokinase domain with small molecule inhibitors
.
Methods in Enzymology
vol.
667
,
455
-
505
.
Motta S, Pandini A, Fornili A, Bonati L
(
2021
)
.
Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks
.
Journal of Chemical Theory and Computation
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 B-D, Fornili A
(
2018
)
.
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
.
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
,
Carluccio C, Fraternali F, Salvatore F, Fornili A, Zagari A
(
2015
)
.
Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylase
.
Journal of Biomolecular Structure and Dynamics
vol.
34
,
(
3
)
497
-
507
.
Lu H-C, Chung SS, Fornili A, Fraternali F
(
2015
)
.
Anatomy of protein disorder, flexibility and disease-related mutations
.
Frontiers in Molecular Biosciences
vol.
2
,
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
.
The 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 P-F, 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
)
no
-
no
.
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 Cl2AlH-catalyzed ring-opening of 2-substituted 1,3-dioxolanes
.
Tetrahedron Letters
vol.
46
,
(
11
)
1837
-
1840
.
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
.
Computational and Theoretical Chemistry
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
)
no
-
no
.
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
.
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
.
Morelli CF, Fornili A, Sironi M, Durı̀ L, Speranza G, Manitto P
(
2002
)
.
Regio- and diastereoselectivity in TiCl4-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
.