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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


    QMRO: qmroHref
  • Tiberti M, Lechner B-D, Fornili A (2018). Binding Pockets Under Mechanical Stress. nameOfConference


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


    QMRO: qmroHref
  • 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


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


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


    QMRO: qmroHref
  • 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


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


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


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


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


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


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


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


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


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


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


    QMRO: qmroHref
  • 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


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


    QMRO: qmroHref
  • 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


    QMRO: qmroHref
  • Pandini A, Fornili A, Kleinjung J (2010). Structural alphabets derived from attractors in conformational space. nameOfConference


    QMRO: qmroHref
  • Fornili A, Pandini A, Fraternali F (2010). Interface Dynamics In Hub Proteins. nameOfConference


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


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


    QMRO: qmroHref
  • 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


    QMRO: qmroHref
  • 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


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


    QMRO: qmroHref
  • 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


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


    QMRO: qmroHref
  • 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


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


    QMRO: qmroHref
  • 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


    QMRO: qmroHref
  • 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


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


    QMRO: qmroHref
  • 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


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


    QMRO: qmroHref

Supervision

Current PhD opportunities

  • Computational modelling of protein dynamics in heart disease

PhD supervision

  • Fariha Akter
  • Anna Antonovic
  • Christos Matsingos