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.
Research group website: afornililab.wordpress.com
Publications
Publications of specific relevance to the Centre for Chemical Research2025
Pathogenic TNNT1 variants are associated with aberrant thin filament compliance and myofibre hyper‐contractilityLaitila J Lewis CTA Hessel AL Primiano G Hernandez‐Lain A Fiorillo C Lawlor MW Ottenheijm CAC et al.
The Journal of Physiology, Wiley vol. 603 (12), 3533-3550.
05-05-2025
2024
Elucidating the Activation Mechanism of the Proton-sensing GPR68 ReceptorMatsingos C Howell LA McCormick PJ Fornili A
Journal of Molecular Biology, Elsevier vol. 436 (16)
25-06-2024
The Legionella collagen-like protein employs a distinct binding mechanism for the recognition of host glycosaminoglycansRehman S Antonovic AK McIntire IE Zheng H Cleaver L Baczynska M Adams CO Portlock T et al.
Nature Communications, Springer Nature vol. 15 (1)
08-06-2024
N4BP1 functions as a dimerization-dependent linear ubiquitin reader which regulates TNF signallingKliza KW Song W Pinzuti I Schaubeck S Kunzelmann S Kuntin D Fornili A Hofmann K
Cell Death Discovery, Springer Nature vol. 10 (1)
20-04-2024
2023
The Legionella collagen-like protein employs a unique binding mechanism for the recognition of host glycosaminoglycansRehman S Antonovic AK McIntire IE Zheng H Cleaver L Adams CO Portlock T Richardson K et al.
, Cold Spring Harbor Laboratory
10-12-2023
Abnormal myosin post‐translational modifications and ATP turnover time associated with human congenital myopathy‐related RYR1 mutationsSonne A Antonovic AK Melhedegaard E Akter F Andersen JL Jungbluth H Witting N Vissing J et al.
Acta Physiologica, Wiley vol. 239 (2)
21-08-2023
Binding pocket dynamics along the recovery stroke of human β-cardiac myosinAkter F Ochala J Fornili A
Plos Computational Biology, Public Library of Science (Plos) vol. 19 (5)
18-05-2023
A rational approach to selective targeting of skeletal myosinAntonovic AK Ochala J Fornili A
Biophysical Journal, Elsevier vol. 122 (3)
01-02-2023
2022
Comparative study of binding pocket structure and dynamics in cardiac and skeletal myosinAntonovic AK Ochala J Fornili A
Biophysical Journal, Biophysical Society vol. 122 (1), 54-62.
29-11-2022
Targeting the HER3 pseudokinase domain with small molecule inhibitorsColomba A Claus J Gao F George R Fornili A Cameron AJM
Methods in Enzymology, Elsevier vol. 667, 455-505.
01-01-2022
2021
Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural NetworksMotta S Pandini A Fornili A Bonati L
Journal of Chemical Theory and Computation, American Chemical Society
29-03-2021
2020
Heart Failure Drug Modifies the Intrinsic Dynamics of the Pre-Power Stroke State of Cardiac MyosinFornili A Hashem S Davies WG
Journal of Chemical Information and Modeling, American Chemical Society
07-12-2020
Structure and functional analysis of the Legionella pneumophila chitinase ChiA reveals a novel mechanism of metal-dependent mucin degradationRehman S Grigoryeva LS Richardson KH Corsini P White RC Shaw R Portlock TJ Dorgan B et al.
Plos Pathogens, Public Library of Science (Plos) vol. 16 (5)
04-05-2020
Reconstruction of ARNT PAS-B Unfolding Paths by Steered MD and Artificial Neural Network Reveals New Putative Binding ConformationsMotta S Pandini A Fornili A
Biophysical Journal, Biophysical Society vol. 118 (3), 297A-297A.
07-02-2020
2018
Binding Pockets in Proteins Induced by Mechanical Stress.Tiberti M Lechner B-D Fornili A
Journal of Chemical Theory and Computation, American Chemical Society (Acs) vol. 15 (1), 1-6.
10-12-2018
Allosteric Modulation of Cardiac Myosin Dynamics by Omecamtiv MecarbilHashem S Tiberti M Fornili A
Biophysical Journal. vol. 114 (3), 36a-37a.
01-02-2018
In Silico Identification of Rescue Sites by Double Force ScanningTiberti M Pandini A Fraternali F Fornili A
Biophysical Journal. vol. 114 (3)
01-02-2018
Binding Pockets Under Mechanical StressTiberti M Fornili A
Biophysical Journal. vol. 114 (3)
01-02-2018
2017
Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbilHashem S Tiberti M Fornili A
Plos Computational Biology vol. 13 (11), e1005826-e1005826.
06-11-2017
In silico identification of rescue sites by double force scanningTiberti M Pandini A Fraternali F FORNILI A
Bioinformatics, Oxford University Press (OUP)
14-08-2017
2016
Using Local States To Drive the Sampling of Global Conformations in ProteinsPandini A Fornili A
Journal of Chemical Theory and Computation, American Chemical Society (Acs) vol. 12 (3), 1368-1379.
12-02-2016
Effect of RlC N-Terminal Tails on the Structure and Dynamics of Cardiac MyosinFornili A Rostkova E Fraternali F Pfuhl M
Biophysical Journal. vol. 110 (3)
01-02-2016
Biasing the Sampling of Local States to Drive the Exploration of Global Conformations in ProteinsPandini A Fornili A
Biophysical Journal. vol. 110 (3), 187a-188a.
01-02-2016
2015
Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylaseCarluccio C Fraternali F Salvatore F Fornili A Zagari A
Journal of Biomolecular Structure and Dynamics, Taylor & Francis vol. 34 (3), 497-507.
19-10-2015
Anatomy of protein disorder, flexibility and disease-related mutationsLu H-C Chung SS Fornili A Fraternali F
Frontiers in Molecular Biosciences, Frontiers vol. 2
12-08-2015
2014
Phosphorylation Modulates the Dynamics of the N-Terminal Tail in Cardiac RLCFORNILI A Rostkova E Fraternali F Pfuhl M
Biophysical Journal, Biophysical Society vol. 106 (2), 33A-33A.
01-01-2014
Gsatools: Analysis of Allosteric Communication and Functional Local Motions using a Structural AlphabetPandini A Fornili A Fraternali F Kleinjung J
Biophysical Journal. vol. 106 (2)
01-01-2014
2013
Structural features of the regulatory ACT domain of phenylalanine hydroxylaseCarluccio C Fraternali F Salvatore F Fornili A Zagari A
Plos One, Public Library of Science vol. 8 (11)
14-11-2013
Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensemblesFornili A Pandini A Lu H-C Fraternali F
Journal of Chemical Theory and Computation, American Chemical Society vol. 9 (11), 5127-5147.
12-11-2013
GSATools: Analysis of allosteric communication and functional local motions using a structural alphabetPandini A Fornili A Fraternali F Kleinjung J
Bioinformatics, Oxford Journals vol. 29 (16), 2053-2055.
15-08-2013
A pH-Regulated Quality Control Cycle for Surveillance of Secretory Protein AssemblyVavassori S Cortini M Masui S Sannino S Anelli T Caserta IR Fagioli C Mossuto MF et al.
Molecular Cell, Elsevier/Science Direct vol. 50 (6), 783-792.
27-06-2013
Decrypting prion protein conversion into a β-rich conformer by molecular dynamicsChakroun N Fornili A Prigent S Kleinjung J Dreiss CA Rezaei H Fraternali F
Journal of Chemical Theory and Computation, American Chemical Society vol. 9 (5), 2455-2465.
14-05-2013
Protein-Protein interaction networks studies and importance of 3D structure knowledgeLu H-C Fornili A Fraternali F
Expert Review of Proteomics, Informa Healthcare vol. 10 (6), 511-520.
01-01-2013
2012
Detection of allosteric signal transmission by information-theoretic analysis of protein dynamicsPandini A Fornili A Fraternali F Kleinjung J
Faseb Journal, American Societies For Experimental Biology vol. 26 (2), 868-881.
01-02-2012
Protein-water interactions in MD simulations: POPS/POPSCOMP solvent accessibility analysis, solvation forces and hydration sitesFornili A Autore F Chakroun N Martinez P Fraternali F
Methods in Molecular Biology, Springer Verlag vol. 819, 375-392.
01-01-2012
Intrinsic Dynamics of the Regulatory Light Chain: Implications on Muscle ContractionFornili A Pfuhl M
Biophysical Journal. vol. 102 (3)
01-01-2012
Detection of Allosteric Signal Transmission by Information-Theoretic Analysis of Protein DynamicsPandini A Fornili A Fraternali F Kleinjung J
Biophysical Journal. vol. 102 (3)
01-01-2012
2010
Energy landscapes associated with macromolecular conformational changes from endpoint structuresFornili A Giabbai B Garau G Degano M
Journal of The American Chemical Society, American Chemical Society vol. 132 (49), 17570-17577.
15-12-2010
In silico phosphorylation of the autoinhibited form of p47phox: Insights into the mechanism of activationAutore F Pagano B Fornili A Rittinger K Fraternali F
Biophysical Journal, Elsevier/Science Direct vol. 99 (11), 3716-3725.
01-12-2010
Structural alphabets derived from attractors in conformational spacePandini A Fornili A Kleinjung J
Bmc Bioinformatics, Biomed Central vol. 11
20-02-2010
Interface Dynamics In Hub ProteinsFornili A Pandini A
Biophysical Journal. vol. 98 (3)
01-01-2010
2008
Structural Basis for Substrate Specificity in Group I Nucleoside Hydrolases ,Iovane E Giabbai B Muzzolini L Matafora V Fornili A
Biochemistry, American Chemical Society (Acs) vol. 47 (15), 4418-4426.
25-03-2008
2007
Accurate Description of Nitrogenous Base Flexibility in Classical Molecular Dynamics Simulations of Nucleotides Bound to ProteinsFornili A Sironi M
The Journal of Physical Chemistry B, American Chemical Society (Acs) vol. 111 (23), 6297-6302.
18-05-2007
Removing extra frontier parameters in QM/MM methods : a tentative with the Local Self-Consistent Field approachLoos P-F FORNILI A Sironi M NA
Computing Letters, Brill vol. 3 (2), 473-486.
01-01-2007
2006
Frozen core orbitals as an alternative to specific frontier bond potential in hybrid Quantum Mechanics/Molecular Mechanics methodsFornili A Loos P-F Sironi M
Chemical Physics Letters, Elsevier vol. 427 (1-3), 236-240.
01-08-2006
On the suitability of strictly localized orbitals for hybrid QM/MM calculationsFornili A Moreau Y Sironi M
Journal of Computational Chemistry, Wiley vol. 27 (4), 515-523.
27-01-2006
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.Morelli CF Fornili A Sironi M Speranza G
Cheminform, Wiley vol. 36 (27), no-no.
16-06-2005
Optimal virtual orbitals to relax wave functions built up with transferred extremely localized molecular orbitalsGenoni A Fornili A
Journal of Computational Chemistry, Wiley vol. 26 (8), 827-835.
06-04-2005
Evidence for a nucleophilic anti-attack on the cleaved C(2)–oxygen bond in Cl2AlH-catalyzed ring-opening of 2-substituted 1,3-dioxolanesMorelli CF Fornili A Durì L Speranza G
Tetrahedron Letters, Elsevier vol. 46 (11), 1837-1840.
01-03-2005
2003
Determination of extremely localized molecular orbitals and their application to quantum mechanics/molecular mechanics methods and to the study of intramolecular hydrogen bondingFornili A Raimondi M
Computational and Theoretical Chemistry, Elsevier vol. 632 (1-3), 157-172.
01-08-2003
Regio‐ and Diastereoselectivity in TiCl4‐Promoted Reduction of 2‐Aryl‐Substituted cis‐4‐Methyl‐5‐trifluoromethyl‐1,3‐dioxolanes.Morelli CF Fornili A Sironi M Speranza G
Cheminform, Wiley vol. 34 (15), no-no.
21-03-2003
Molecular dynamics simulation of aqueous solutions of trimethylamine-N-oxide and tert-butyl alcoholFornili A Civera M Sironi M Fornili SL
Physical Chemistry Chemical Physics, Royal Society of Chemistry (Rsc) vol. 5 (21), 4905-4910.
01-01-2003
Molecular dynamics simulation of aqueous solutions of glycine betaineCivera M Fornili A Sironi M
Chemical Physics Letters, Elsevier vol. 367 (1-2), 238-244.
01-01-2003
2002
Regio- and diastereoselectivity in TiCl4-promoted reduction of 2-aryl-substituted cis-4-methyl-5-trifluoromethyl-1,3-dioxolanesMorelli CF Fornili A Sironi M Durı̀ L Manitto P
Tetrahedron Asymmetry, Elsevier vol. 13 (23), 2609-2618.
01-11-2002
2001
Water interaction with glycine betaine: A hybrid QM/MM molecular dynamics simulation.FORNILI A
Physical Chemistry Chemical Physics, Royal Society of Chemistry vol. 3, 1081-1085.
01-01-2001
N4BP1 is dimerization-dependent linear ubiquitin reader regulating TNFR1 signalling through linear ubiquitin binding and Caspase-8-mediated processingKliza K Song W Pinzuti I Schaubeck S Kunzelmann S Kuntin D Fornili A Pandini A et al.
In Biorxiv
Structure and functional analysis of the Legionella chitinase ChiA reveals a novel mechanism of metal-dependent mucin degradationIn Biorxiv
Elucidating the activation mechanism of the proton-sensing GPR68 receptorMatsingos C Howell LA McCormick PJ Fornili A
In Biorxiv
Grants
Grants of specific relevance to the Centre for Chemical ResearchBBSRC 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
Grant Summary
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 Chandran Darbari and Arianna Fornili
£579,168 Biotechnology and Biological Sciences Research Council
28-10-2022 - 31-03-2026
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
£123,829 BBSRC Biotechnology and Biological Sciences Research Council
01-10-2022 - 30-09-2026
Structural Bioinformatics and chemogenomics approachesArianna Fornili
£21,600 Nxera Pharma UK Ltd
26-09-2022 - 25-09-2026
Developing novel antibody tools to modulate GPR20Andrew Tinker, Arianna Fornili, Ahuva Nissim and Peter McCormick
£74,767 Barts and the London Charity
01-02-2024 - 30-06-2025
Rational design of selective modulators of skeletal myosinArianna Fornili
£109,387 Muscular Dystrophy Association
01-01-2020 - 31-12-2023
RSC UG Bursary: William George DavisArianna Fornili
£2,200 RSC The Royal Society of Chemistry
01-06-2019 - 31-08-2019
Research Group
PhD Students
- Sophia Ber
Insights Into The Gating Mechanism of Two-Pore Potassium Channels - Charlea Clarke
Structural and Biochemical Characterisation of B12-Binding Proteins in Bacteroides Thetaiotaomicron - Dave Dai
Cheminformatics and Machine Learning Approaches For Gpcr Computer-Aided Drug Design - Azaan Hafeez
Chem Project - Stylianos Iliadis
Modelling G Protein Coupled Receptors in Vitro - Ka Fu Man
Computational Modelling of Biological Systems For The Treatment of Congenital Myopathies and Cardiovascular Diseases - Siyu Meng
Designing a Novel Thermal Insulation System With Advanced Artificial Intelligence Techniques - Zainab Shafique
Chem Project - Steven Sun
Using Computational and Experimental Methods to Predict and Test Novel Neuropeptide-Receptor Partnerships - Yu-Yuan Yang
Machine Learning For Structure-Based Drug & Biologic Discovery—Binding Pocket Classification For Structure-Based Drug Discovery
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