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School of Physical and Chemical Sciences

Dr Arianna Fornili

Arianna

Senior Lecturer in Computational Organic Chemistry and Programme Director for Chemical Research MSc.

Email: a.fornili@qmul.ac.uk
Telephone: +44 (0)20 7882 8446
Room Number: Room G04, Joseph Priestley Building

Undergraduate Teaching

  • Essential Skills for Chemists (Tutorials) (CHE100)
  • Pharmaceutical Chemistry (CHE206A)

  • Pharmaceutical Chemistry (CHE206B)

  • Introduction to Scientific Programming (SBC5291)

  • Introduction to Scientific Programming (SBC5292)

Postgraduate Teaching

Programme Director for Chemical Research MSc.

Research

Research Interests:

My research activity is focused on the computational study of protein dynamics and its relationship to protein function.

The main interest of the group is the study of structural, dynamical and mechanical properties of proteins from the cardiac muscle. Heart contraction arises from a complex interplay of precisely timed molecular motions and the identification of new therapeutic targets for cardiomyopathies relies on a deep understanding of these mechanisms. Combining Molecular Modelling, Molecular Dynamics simulation and Bioinformatics techniques, we investigate how post-translational modifications and cardiomyopathy-related mutations affect the protein motion and stability.

The group is also involved in the development of computational methods for the study of conformational transitions in proteins. In addition to promoting the motion of molecular motors, conformational changes can be essential for many protein functions and they are often required for protein-protein interaction and allosteric regulation. The group aims at improving both the sampling and the detection of biologically relevant conformational transitions, which are usually beyond the timescale of traditional molecular simulations.

Research Department

Publications

Browse a list of publications by Arianna Fornili

    • Motta S, Pandini A, Fornili A et al. (2021), Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks $nameOfConference


    • Fornili A, Hashem S, Davies WG (2020), Heart Failure Drug Modifies the Intrinsic Dynamics of the Pre-Power Stroke State of Cardiac Myosin $nameOfConference


    • Rehman S, Grigoryeva LS, Richardson KH et al. (2020), Structure and functional analysis of the Legionella pneumophila chitinase ChiA reveals a novel mechanism of metal-dependent mucin degradation $nameOfConference


    • Motta S, Pandini A, Fornili A et al. (2020), Reconstruction of ARNT PAS-B Unfolding Paths by Steered MD and Artificial Neural Network Reveals New Putative Binding Conformations $nameOfConference


    • Tiberti M, Lechner BD, Fornili A (2019), Binding Pockets in Proteins Induced by Mechanical Stress $nameOfConference


    • Hashem S, Tiberti M, Fornili A (2018), Allosteric Modulation of Cardiac Myosin Dynamics by Omecamtiv Mecarbil $nameOfConference


    • Tiberti M, Lechner B-D, Fornili A (2018), Binding Pockets Under Mechanical Stress $nameOfConference


    • Tiberti M, Pandini A, Fraternali F et al. (2018), In Silico Identification of Rescue Sites by Double Force Scanning $nameOfConference


    • Hashem S, Tiberti M, Fornili A (2017), Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil $nameOfConference


    • Tiberti M, Pandini A, Fraternali F et al. (publicationYear), In silico identification of rescue sites by double force scanning $nameOfConference


    • Pandini A, Fornili A (2016), Using Local States to Drive the Sampling of Global Conformations in Proteins $nameOfConference


    • Carluccio C, Fraternali F, Salvatore F et al. (2016), Towards the identification of the allosteric Phe-binding site in phenylalanine hydroxylase $nameOfConference


    • Pandini A, Fornili A (2016), Biasing the Sampling of Local States to Drive the Exploration of Global Conformations in Proteins $nameOfConference


    • Fornili A, Rostkova E, Fraternali F et al. (2016), Effect of RlC N-Terminal Tails on the Structure and Dynamics of Cardiac Myosin $nameOfConference


    • Lu HC, Chung SS, Fornili A et al. (2015), Anatomy of protein disorder, flexibility and disease-related mutations $nameOfConference


    • Pandini A, Fornili A, Fraternali F et al. (2014), Gsatools: Analysis of Allosteric Communication and Functional Local Motions using a Structural Alphabet $nameOfConference


    • FORNILI A, Rostkova E, Fraternali F et al. (2014), Phosphorylation Modulates the Dynamics of the N-Terminal Tail in Cardiac RLC $nameOfConference


    • Carluccio C, Fraternali F, Salvatore F et al. (2013), Structural features of the regulatory ACT domain of phenylalanine hydroxylase $nameOfConference


    • Fornili A, Pandini A, Lu H-C et al. (2013), Specialized dynamical properties of promiscuous residues revealed by simulated conformational ensembles $nameOfConference


    • Pandini A, Fornili A, Fraternali F et al. (2013), GSATools: Analysis of allosteric communication and functional local motions using a structural alphabet $nameOfConference


    • Vavassori S, Cortini M, Masui S et al. (2013), A pH-Regulated Quality Control Cycle for Surveillance of Secretory Protein Assembly $nameOfConference


    • Chakroun N, Fornili A, Prigent S et al. (2013), Decrypting prion protein conversion into a β-rich conformer by molecular dynamics $nameOfConference


    • Lu H-C, Fornili A, Fraternali F (2013), Protein-Protein interaction networks studies and importance of 3D structure knowledge $nameOfConference


    • Pandini A, Fornili A, Fraternali F et al. (2012), Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics $nameOfConference


    • Pandini A, Fornili A, Fraternali F et al. (2012), Detection of Allosteric Signal Transmission by Information-Theoretic Analysis of Protein Dynamics $nameOfConference


    • Fornili A, Pfuhl M, Fraternali F (2012), Intrinsic Dynamics of the Regulatory Light Chain: Implications on Muscle Contraction $nameOfConference


    • 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 $nameOfConference


    • Fornili A, Giabbai B, Garau G et al. (2010), Energy landscapes associated with macromolecular conformational changes from endpoint structures $nameOfConference


    • Autore F, Pagano B, Fornili A et al. (2010), In silico phosphorylation of the autoinhibited form of p47phox: Insights into the mechanism of activation $nameOfConference


    • Pandini A, Fornili A, Kleinjung J (2010), Structural alphabets derived from attractors in conformational space $nameOfConference


    • Fornili A, Pandini A, Fraternali F (2010), Interface Dynamics In Hub Proteins $nameOfConference


    • Iovane E, Giabbai B, Muzzolini L et al. (2008), Structural basis for substrate specificity in group I nucleoside hydrolases $nameOfConference


    • Fornili A, Sironi M, Degano M (2007), Accurate description of nitrogenous base flexibility in classical molecular dynamics simulations of nucleotides bound to proteins $nameOfConference


    • 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 $nameOfConference


    • 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 $nameOfConference


    • Fornili A, Moreau Y, Sironi M et al. (2006), On the suitability of strictly localized orbitals for hybrid QM/MM calculations $nameOfConference


    • Morelli CF, Fornili A, Sironi M et al. (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. $nameOfConference


    • Genoni A, Fornili A, Sironi M (2005), Optimal virtual orbitals to relax wave functions built up with transferred extremely localized molecular orbitals $nameOfConference


    • Morelli CF, Fornili A, Sironi M et al. (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 $nameOfConference


    • Fornili A, Civera M, Sironi M et al. (2003), Molecular dynamics simulation of aqueous solutions of trimethylamine-N- oxide and tert-butyl alcohol $nameOfConference


    • 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 $nameOfConference


    • Morelli CF, Fornili A, Sironi M et al. (2003), Regio‐ and Diastereoselectivity in TiCl4‐Promoted Reduction of 2‐Aryl‐Substituted cis‐4‐Methyl‐5‐trifluoromethyl‐1,3‐dioxolanes. $nameOfConference


    • Civera M, Fornili A, Sironi M et al. (2003), Molecular dynamics simulation of aqueous solutions of glycine betaine $nameOfConference


    • Morelli CF, Fornili A, Sironi M et al. (2002), Regio- and diastereoselectivity in TiCl4-promoted reduction of 2-aryl-substituted cis-4-methyl-5-trifluoromethyl-1,3-dioxolanes $nameOfConference


    • FORNILI A (2001), Water interaction with glycine betaine: A hybrid QM/MM molecular dynamics simulation. $nameOfConference


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