Computational Biophysics at Maynooth University

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• E. Fadda* and MG. Nixon "The transient manifold structure of the p53 extreme C-terminal domain: insight into disorder, recognition, and binding promiscuity by molecular dynamics simulations" PCCP (2017), 19(32):21287-21296

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• E. Fadda* "Role of the XPA protein in the NER pathway: A perspective on the function of structural disorder in macromolecular assembly" Computational and Structural Biotechnology Journal (2016), 14, 78–85

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• Ursula Sheridan, John F. Gallagher, Elisa Fadda, Morten J. Bjerrum, and John McGinley, "Synthesis and characterisation of new copper(II) coordination polymers constructed from pyrazine–tetrazole ligands with the formation of a water cluster", Supramolecular Chemistry (2016), 28(7-8), 707-719

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• Niall J. Maher,  Haowen Diao, Justine O'Sullivan, Elisa Fadda, Frances Heaney, John McGinley "Lower rim isoxazole-calix[4]arene derivatives as fluorescence sensors for copper(II) ions" Tetrahedron (2015), 71(49), 9223–9233

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• Gerard L. Brien, Evan Healy, Emilia Jerman, Eric Conway, Elisa Fadda, Darragh O'Donovan, Andrei V. Krivtsov, Alan M. Rice, Conor J. Kearney, Andrew Flaus, Simon S. McDade, Seamus J. Martin, Aoife McLysaght, David J. O'Connell, Scott A. Armstrong, and Adrian P. Bracken "A chromatin-independent role of Polycomb-like 1 to stabilize p53 and promote cellular quiescence", Genes and Development (2015), 29(21), 2231-43 DOI:10.1101/gad.267930.115

 

• E. Fadda* “The role of conformational selection in the molecular recognition of the wild type and mutants XPA67-80 peptides by ERCC1”, PROTEINS: Structure, Function and Bioinformatics (2015), 83(7):1341-51 DOI: 10.1002/prot.24825

 

• J.A. Hadden, M. Tessier, E. Fadda and R.J. Woods “Calculating binding free energies for protein-carbohydrate complexes” In: Methods in Molecular Biology: Glycoinformatics, Ed. M. Frank, (Clifton, N.J.) 1273: 431-465, January 2015

 

• J.C. Martin, E. Fadda, K. Ito, and R.J Woods “Defining the Structural Origin of the Substrate Sequence Independence of O-GlcNAcase Using a Combination of Molecular Docking and Dynamics Simulation”, Glycobiology (2014), 24(1), 85-96 

 

• O.C. Grant, H.M. Smith, D. Firsova, E. Fadda, and R.J. Woods “Presentation, Presentation, Presentation! Molecular Level Insight into Linker Effects on Glycan Array Screening Data” Glycobiology (2014), 24(1), 17-25

 

• N.T. Wood, E. Fadda, R. Davis, O.C. Grant, J.C Martin, R.J. Woods, and S.A. Travers “The Influence of N-Linked Glycans on the Molecular Dynamics of the HIV-1 gp120 V3 Loop”, PLoS One (2013), 8(11), e80301

 

• E. Fadda* “Conformational determinants for the recruitment of ERCC1 by XPA in the Nucleotide Excision Repair (NER) pathway: Structure and dynamics of the XPA binding motif.” Biophys. J. (2013), 104(11), 2503-2511

 

• E. Fadda* and R.J. Woods “Contribution of the empirical dispersion correction on the conformation of short alanine peptides obtained by gas-phase QM calculations.” Can. J. Chem. (2013), 91(9), 859-865, (Issue in Honor of Prof. D.R. Salahub) 

 

• E. Fadda and R.J. Woods “On the role of water models in quantifying the standard binding free energy of highly conserved water molecules in proteins: the case of Concanavalin A” J. Chem. Theo. Comput. (2011), 7(10), 3391-3398

 

• R. Henry, D. Caplan, E. Fadda and R. Pomès “Molecular Basis for Proton Uptake in Single and Double Mutants of Cytochrome c Oxidase.", J. Phys. Condens. Matter, (2011), 23(23), 234102

 

• R. Kadirvelraj, O.C. Grant, I.J. Goldstein, H. Tateno, E. Fadda and R.J. Woods, “Structure of a Human-type Influenza Epitope [Neu5Ac-a-(2,6)-Gal-b-(1,4)-GlcNAc] Bound to Polyporus squamosus Lectin”, Glycobiology (2011), 21(7), 973-984

 

• E. Fadda*, and R. Pomès “On the Molecular Basis of Uracil Recognition in DNA: Comparative study of T:A vs. U:A Structure, Dynamics and Open Base Pair Kinetics”, Nucleic Acids Res. (2011), 39(2), 767-780

 

• E. Fadda, R.J. Woods “Molecular Simulation of Carbohydrates and Protein-Carbohydrate Interactions: Motivations, Issues and Prospects” Drug Discov. Today (2010), 15, 596-609

 

• E. Fadda*, C.-H. Yu, and R. Pomès “Electrostatic Control of Proton Pumping in Cytochrome c Oxidase”, Biochim. Biophys. Acta: Bioenerg., (2008) 1777, 277

 

• E. Fadda, N. Chakrabarti, and R. Pomès “Acidity of a Cu-bound Histidine in the Binuclear Center of Cytochrome c Oxidase” J. Phys. Chem. B (2005), 109, 22629;  and “Reply to the Comment on “Acidity of a Cu-Bound Histidine in the Binuclear Center of Cytochrome c Oxidase””J. Phys. Chem. B (2006), 110, 17288

 

• E.Fadda*, M.E. Casida, and D.R. Salahub: “NMR Shieldings from Sum-Over-States Density-Functional Perturbation-Theory: Further Testing of the “Loc.3” Approximation”, J. Chem. Phys., (2003) 118, 6758

 

• E. Fadda*, M.E. Casida and D.R. Salahub: “14,15N NMR Shielding Constants from Density-Functional Theory”, J. Phys. Chem. A (2003), 107, 9924

 

• E. Fadda, M.E. Casida and D.R. Salahub: “Time-Dependent Density-Functional Theory as a Foundation for a Firmer Understanding of Sum-Over-States Density-Functional Perturbation-Theory: “Loc.3” Approximation”, Int. J. Quantum. Chem. (2003), 91, 68