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School of Physical and Chemical Sciences
  1. School of Physical and Chemical Sciences
  2. Physical and Computational Chemistry
  3. Research
  4. Biomolecular Simulations

Biomolecular Simulations

Biomolecular Modelling

Research in this section focuses on the computational study of protein dynamics and its relationship to protein function. Systems currently under investigation range from muscle proteins to GPCR receptors and to kinases. The section is also involved in the development of general methods for the modelling of conformational transitions in proteins and of protein-ligand interactions.

Techniques: Molecular Dynamics simulations of biomolecules, Homology Modelling, Molecular Docking, Virtual Screening.

Keywords: protein dynamics, muscle proteins, myosin modulators, in silico drug design, binding pocket dynamics.

Recent Publications

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
10.1021/acs.jctc.0c01308
https://qmro.qmul.ac.uk/xmlui/handle/123456789/72283

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
10.1021/acs.jcim.0c00953
https://qmro.qmul.ac.uk/xmlui/handle/123456789/69421

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)
10.1371/journal.ppat.1008342
https://qmro.qmul.ac.uk/xmlui/handle/123456789/64461

Tiberti M, Lechner BD, Fornili A (2019). Binding Pockets in Proteins Induced by Mechanical Stress. Journal of Chemical Theory and Computation vol. 15, (1) 1-6.
10.1021/acs.jctc.8b00755
https://qmro.qmul.ac.uk/xmlui/handle/123456789/54640

Hashem S, Tiberti M, Fornili A (2017) . Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil . PLOS Computational Biology vol. 13, (11) e1005826-e1005826.
10.1371/journal.pcbi.1005826
https://qmro.qmul.ac.uk/xmlui/handle/123456789/28677

Tiberti M, Pandini A, Fraternali F, FORNILI A (2017) . In silico identification of rescue sites by double force scanning. Bioinformatics
10.1093/bioinformatics/btx515
https://qmro.qmul.ac.uk/xmlui/handle/123456789/25449

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 .
10.1021/acs.jctc.5b00992
https://qmro.qmul.ac.uk/xmlui/handle/123456789/28561

Allosteric modulation of cardiac myosin dynamics

From: S. Hashem, M. Tiberti, A. Fornili (2017). Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil. PLoS Computational Biology 13: e1005826. 10.1371/journal.pcbi.1005826

Binding Pockets in Proteins Induced by Mechanical Stress

From: M. Tiberti, B.-D. Lechner, A. Fornili (2019). Binding Pockets in Proteins Induced by Mechanical Stress. Journal of Chemical Theory and Computation. 10.1021/acs.jctc.8b00755

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