Dr Arianna Fornili
Reader in Computational Chemistry
Director of The Artificial Intelligence for Drug Discovery MSc programme
School of Physical and Chemical Sciences
Queen Mary University of London
Queen Mary University of London
Research
Molecular dynamics, Protein dynamics, Myosin, Molecular Modelling, Machine Learning, Protein-ligand interactions
Interests
The research activity of the group is focused on the computational study of protein dynamics and its relationship to protein function.One of the main interests of the group is the study of structural, dynamical and mechanical properties of proteins from skeletal and cardiac muscle. The group is also involved in the development of computational methods for the study of conformational transitions in proteins and for advanced analysis of simulation data.
Publications
Publications of specific relevance to the Centre for Chemical Research2024
Matsingos C, Howell LA, McCormick PJ and Fornili A (2024). Elucidating the Activation Mechanism of the Proton-sensing GPR68 Receptor. Journal of Molecular Biology, Elsevier vol. 436 (16) 25-06-2024
Rehman S, Antonovic AK, McIntire IE, Zheng H, Cleaver L, Baczynska M, Adams CO, Portlock T, Richardson K, Shaw R, Oregioni A, Mastroianni G, Whittaker SB-M, Kelly G, Lorenz CD, Fornili A, Cianciotto NP and Garnett JA (2024). The Legionella collagen-like protein employs a distinct binding mechanism for the recognition of host glycosaminoglycans. Nature Communications, Springer Nature vol. 15 (1) 08-06-2024
Kliza KW, Song W, Pinzuti I, Schaubeck S, Kunzelmann S, Kuntin D, Fornili A, Pandini A, Hofmann K, Garnett JA, Stieglitz B and Husnjak K (2024). N4BP1 functions as a dimerization-dependent linear ubiquitin reader which regulates TNF signalling. Cell Death Discovery, Springer Nature vol. 10 (1) 20-04-2024
2023
Rehman S, Antonovic AK, McIntire IE, Zheng H, Cleaver L, Adams CO, Portlock T, Richardson K, Shaw R, Oregioni A, Mastroianni G, Whittaker SB-M, Kelly G, Fornili A, Cianciotto NP and Garnett JA (2023). The Legionella collagen-like protein employs a unique binding mechanism for the recognition of host glycosaminoglycans. 10-12-2023
Sonne A, Antonovic AK, Melhedegaard E, Akter F, Andersen JL, Jungbluth H, Witting N, Vissing J, Zanoteli E, Fornili A and Ochala J (2023). Abnormal myosin post‐translational modifications and ATP turnover time associated with human congenital myopathy‐related RYR1 mutations. Acta Physiologica, Wiley vol. 239 (2) 21-08-2023
Akter F, Ochala J and Fornili A (2023). Binding pocket dynamics along the recovery stroke of human β-cardiac myosin. PLOS Computational Biology, Public Library of Science (PLoS) vol. 19 (5) 18-05-2023
Antonovic AK, Ochala J and Fornili A (2023). A rational approach to selective targeting of skeletal myosin. Biophysical Journal, Elsevier vol. 122 (3) 01-02-2023
2022
Antonovic AK, Ochala J and Fornili A (2022). Comparative study of binding pocket structure and dynamics in cardiac and skeletal myosin. Biophysical Journal, Biophysical Society vol. 122 (1), 54-62. 29-11-2022
Colomba A, Claus J, Gao F, George R, Fornili A and Cameron AJM (2022). Targeting the HER3 pseudokinase domain with small molecule inhibitors. Methods in Enzymology, Elsevier vol. 667, 455-505. 01-01-2022
2021
Motta S, Pandini A, Fornili A and Bonati L (2021). Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks. Journal of Chemical Theory and Computation, American Chemical Society 29-03-2021
2020
Fornili A, Hashem S and 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, American Chemical Society 07-12-2020
Rehman S, Grigoryeva LS, Richardson KH, Corsini P, White RC, Shaw R, Portlock TJ, Dorgan B, Zanjani ZS, Fornili A, Cianciotto NP and Garnett JA (2020). Structure and functional analysis of the Legionella pneumophila chitinase ChiA reveals a novel mechanism of metal-dependent mucin degradation. PLOS Pathogens, Public Library of Science (PLoS) vol. 16 (5) 04-05-2020
Motta S, Pandini A, Fornili A and Bonati L (2020). Reconstruction of ARNT PAS-B Unfolding Paths by Steered MD and Artificial Neural Network Reveals New Putative Binding Conformations. Biophysical Journal, Biophysical Society vol. 118 (3), 297A-297A. 07-02-2020
2018
Tiberti M, Lechner B-D and Fornili A (2018). Binding Pockets in Proteins Induced by Mechanical Stress. Journal of Chemical Theory and Computation, American Chemical Society (ACS) vol. 15 (1), 1-6. 10-12-2018
Hashem S, Tiberti M and Fornili A (2018). Allosteric Modulation of Cardiac Myosin Dynamics by Omecamtiv Mecarbil. 01-02-2018
Tiberti M, Pandini A, Fraternali F and Fornili A (2018). In Silico Identification of Rescue Sites by Double Force Scanning. 01-02-2018
2017
Hashem S, Tiberti M and Fornili A (2017). Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil., Editors: Wei G. PLOS Computational Biology vol. 13 (11), e1005826-e1005826. 06-11-2017
Tiberti M, Pandini A, Fraternali F and FORNILI A (2017). In silico identification of rescue sites by double force scanning. Bioinformatics, Oxford University Press (OUP) 14-08-2017
2016
Pandini A and Fornili A (2016). Using Local States To Drive the Sampling of Global Conformations in Proteins. Journal of Chemical Theory and Computation, American Chemical Society (ACS) vol. 12 (3), 1368-1379. 12-02-2016
Fornili A, Rostkova E, Fraternali F and Pfuhl M (2016). Effect of RlC N-Terminal Tails on the Structure and Dynamics of Cardiac Myosin. 01-02-2016
Pandini A and Fornili A (2016). Biasing the Sampling of Local States to Drive the Exploration of Global Conformations in Proteins. 01-02-2016
2015
Carluccio C, Fraternali F, Salvatore F, Fornili A and Zagari A (2015). Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylase. Journal of Biomolecular Structure and Dynamics, Taylor & Francis vol. 34 (3), 497-507. 19-10-2015
Lu H-C, Chung SS, Fornili A and Fraternali F (2015). Anatomy of protein disorder, flexibility and disease-related mutations. Frontiers in Molecular Biosciences, Frontiers vol. 2 12-08-2015
2014
FORNILI A, Rostkova E, Fraternali F and Pfuhl M (2014). Phosphorylation Modulates the Dynamics of the N-Terminal Tail in Cardiac RLC., Editors: NA . Biophysical Journal, Biophysical Society vol. 106 (2), 33A-33A. 01-01-2014
Pandini A, Fornili A, Fraternali F and Kleinjung J (2014). Gsatools: Analysis of Allosteric Communication and Functional Local Motions using a Structural Alphabet. 01-01-2014
2013
Carluccio C, Fraternali F, Salvatore F, Fornili A and Zagari A (2013). Structural features of the regulatory ACT domain of phenylalanine hydroxylase. PLoS ONE, Public Library of Science vol. 8 (11) 14-11-2013
Fornili A, Pandini A, Lu H-C and Fraternali F (2013). Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles. Journal of Chemical Theory and Computation, American Chemical Society vol. 9 (11), 5127-5147. 12-11-2013
Pandini A, Fornili A, Fraternali F and Kleinjung J (2013). GSATools: Analysis of allosteric communication and functional local motions using a structural alphabet. Bioinformatics, Oxford Journals vol. 29 (16), 2053-2055. 15-08-2013
Vavassori S, Cortini M, Masui S, Sannino S, Anelli T, Caserta IR, Fagioli C, Mossuto MF, Fornili A, vanAnken E, Degano M, Inaba K and Sitia R (2013). A pH-Regulated Quality Control Cycle for Surveillance of Secretory Protein Assembly. Molecular Cell, Elsevier/Science Direct vol. 50 (6), 783-792. 27-06-2013
Chakroun N, Fornili A, Prigent S, Kleinjung J, Dreiss CA, Rezaei H and Fraternali F (2013). Decrypting prion protein conversion into a β-rich conformer by molecular dynamics. Journal of Chemical Theory and Computation, American Chemical Society vol. 9 (5), 2455-2465. 14-05-2013
Lu H-C, Fornili A and Fraternali F (2013). Protein-Protein interaction networks studies and importance of 3D structure knowledge. Expert Review of Proteomics, Informa Healthcare vol. 10 (6), 511-520. 01-01-2013
2012
Pandini A, Fornili A, Fraternali F and Kleinjung J (2012). Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics. FASEB Journal, American Societies for Experimental Biology vol. 26 (2), 868-881. 01-02-2012
Fornili A, Autore F, Chakroun N, Martinez P and Fraternali F (2012). Protein-water interactions in MD simulations: POPS/POPSCOMP solvent accessibility analysis, solvation forces and hydration sites. Methods in Molecular Biology, Springer Verlag vol. 819, 375-392. 01-01-2012
Fornili A, Pfuhl M and Fraternali F (2012). Intrinsic Dynamics of the Regulatory Light Chain: Implications on Muscle Contraction. 01-01-2012
Pandini A, Fornili A, Fraternali F and Kleinjung J (2012). Detection of Allosteric Signal Transmission by Information-Theoretic Analysis of Protein Dynamics. 01-01-2012
2010
Fornili A, Giabbai B, Garau G and Degano M (2010). Energy landscapes associated with macromolecular conformational changes from endpoint structures. Journal of the American Chemical Society, American Chemical Society vol. 132 (49), 17570-17577. 15-12-2010
Autore F, Pagano B, Fornili A, Rittinger K and Fraternali F (2010). In silico phosphorylation of the autoinhibited form of p47phox: Insights into the mechanism of activation. Biophysical Journal, Elsevier/Science Direct vol. 99 (11), 3716-3725. 01-12-2010
Pandini A, Fornili A and Kleinjung J (2010). Structural alphabets derived from attractors in conformational space. BMC Bioinformatics, BioMed Central vol. 11 20-02-2010
2008
Iovane E, Giabbai B, Muzzolini L, Matafora V, Fornili A, Minici C, Giannese F and Degano M (2008). Structural Basis for Substrate Specificity in Group I Nucleoside Hydrolases ,. Biochemistry, American Chemical Society (ACS) vol. 47 (15), 4418-4426. 25-03-2008
2007
Fornili A, Sironi M and 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, American Chemical Society (ACS) vol. 111 (23), 6297-6302. 18-05-2007
Loos P-F, FORNILI A, Sironi M and Assfeld X (2007). Removing extra frontier parameters in QM/MM methods : a tentative with the Local Self-Consistent Field approach., Editors: NA . Computing Letters, Brill vol. 3 (2), 473-486. 01-01-2007
2006
Fornili A, Loos P-F, Sironi M and Assfeld X (2006). Frozen core orbitals as an alternative to specific frontier bond potential in hybrid Quantum Mechanics/Molecular Mechanics methods. Chemical Physics Letters, Elsevier vol. 427 (1-3), 236-240. 01-08-2006
Fornili A, Moreau Y, Sironi M and Assfeld X (2006). On the suitability of strictly localized orbitals for hybrid QM/MM calculations. Journal of Computational Chemistry, Wiley vol. 27 (4), 515-523. 27-01-2006
2005
Morelli CF, Fornili A, Sironi M, Duri L, Speranza G and 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, Wiley vol. 36 (27), no-no. 16-06-2005
Genoni A, Fornili A and Sironi M (2005). Optimal virtual orbitals to relax wave functions built up with transferred extremely localized molecular orbitals. Journal of Computational Chemistry, Wiley vol. 26 (8), 827-835. 06-04-2005
Morelli CF, Fornili A, Sironi M, Durì L, Speranza G and 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, Elsevier vol. 46 (11), 1837-1840. 01-03-2005
2003
Fornili A, Sironi M and 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, Elsevier vol. 632 (1-3), 157-172. 01-08-2003
Morelli CF, Fornili A, Sironi M, Duri L, Speranza G and Manittoa P (2003). Regio‐ and Diastereoselectivity in TiCl4‐Promoted Reduction of 2‐Aryl‐Substituted cis‐4‐Methyl‐5‐trifluoromethyl‐1,3‐dioxolanes. ChemInform, Wiley vol. 34 (15), no-no. 21-03-2003
Fornili A, Civera M, Sironi M and Fornili SL (2003). Molecular dynamics simulation of aqueous solutions of trimethylamine-N-oxide and tert-butyl alcohol. Physical Chemistry Chemical Physics, Royal Society of Chemistry (RSC) vol. 5 (21), 4905-4910. 01-01-2003
Civera M, Fornili A, Sironi M and Fornili SL (2003). Molecular dynamics simulation of aqueous solutions of glycine betaine. Chemical Physics Letters, Elsevier vol. 367 (1-2), 238-244. 01-01-2003
2002
Morelli CF, Fornili A, Sironi M, Durı̀ L, Speranza G and Manitto P (2002). Regio- and diastereoselectivity in TiCl4-promoted reduction of 2-aryl-substituted cis-4-methyl-5-trifluoromethyl-1,3-dioxolanes. Tetrahedron Asymmetry, Elsevier vol. 13 (23), 2609-2618. 01-11-2002
2001
FORNILI A (2001). Water interaction with glycine betaine: A hybrid QM/MM molecular dynamics simulation. Physical Chemistry Chemical Physics, Royal Society of Chemistry vol. 3, 1081-1085. 01-01-2001
Grants
Grants of specific relevance to the Centre for Chemical ResearchDeveloping novel antibody tools to modulate GPR20Andrew Tinker, Arianna Fornili, Ahuva Nissim and Peter McCormick
£74,767 Barts and the London Charity (01-02-2024 - 31-03-2025)
BBSRC AIDD CTP CASE Award: Yu-Yuan YangRichard Pickersgill and Arianna Fornili
£8,600 Evotec EVOTEC (UK) LIMITED (01-10-2023 - 30-09-2027)
TG: Cheminformatics and machine learning approaches for GPCR computer aided drug designArianna Fornili
£125,091 BBSRC Biotechnology and Biological Sciences Research Council (01-10-2023 - 30-09-2027)
Wei Dai Studentship - Sosei HeptaresArianna Fornili and Emma Tjong
£21,600 Nxera Pharma UK Ltd (01-10-2023 - 30-09-2027)
Discovering missing links in neuropeptide evolution and functionMaurice Elphick and Arianna Fornili
£576,040 BBSRC Biotechnology and Biological Sciences Research Council (01-06-2023 - 31-05-2026)
The cardiovascular function of the orphan G-protein coupled receptor GPR20Andrew Tinker, Peter McCormick, Arianna Fornili and Patricia Munroe
£307,773 BHF British Heart Foundation (01-05-2023 - 30-04-2026)
Structure of the assembly platform of the type II secretion systemRichard Pickersgill, Vidya Darbari and Arianna Fornili
£579,168 BBSRC Biotechnology and Biological Sciences Research Council (28-10-2022 - 27-10-2025)
CTP Training Grant:Arianna Fornili
£124,909 BBSRC Biotechnology and Biological Sciences Research Council (01-10-2022 - 30-09-2026)
Structural bioinformatics and chemogenomics approaches to navigate GPCR ligand interaction space - CTPArianna Fornili
£123,282 BBSRC Biotechnology and Biological Sciences Research Council (01-10-2022 - 30-09-2026)
Structural Bioinformatics and chemogenomics approachesArianna Fornili
£21,600 Sosei Heptares (26-09-2022 - 25-09-2026)
Rational design of selective modulators of skeletal myosinArianna Fornili
£109,387 MDA Muscular Dystrophy Association (01-01-2020 - 31-12-2023)