Publications (19) NATALIA DIAZ FERNANDEZ publications View referenced research data.

filter_list Biochemistry

2021

  1. Influence of charge configuration on substrate binding to SARS-CoV-2 main protease

    Chemical Communications, Vol. 57, Núm. 43, pp. 5314-5317

2020

  1. SARS-CoV-2 Main Protease: A Molecular Dynamics Study

    Journal of Chemical Information and Modeling, Vol. 60, Núm. 12, pp. 5815-5831

2013

  1. Unraveling the molecular structure of the catalytic domain of matrix metalloproteinase-2 in complex with a triple-helical peptide by means of molecular dynamics simulations

    Biochemistry, Vol. 52, Núm. 47, pp. 8556-8569

2012

  1. Alternative interdomain configurations of the full-length MMP-2 enzyme explored by molecular dynamics simulations

    Journal of Physical Chemistry B, Vol. 116, Núm. 9, pp. 2677-2686

2010

  1. Interdomain conformations in the full-length MMP-2 enzyme explored by protein-protein docking calculations using pyDock

    Journal of Chemical Theory and Computation, Vol. 6, Núm. 7, pp. 2204-2213

  2. Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: Molecular dynamics and QM/MM calculations

    Proteins: Structure, Function and Bioinformatics, Vol. 78, Núm. 1, pp. 1-11

  3. Understanding regioselective cleavage in peptide hydrolysis by a palladium(II) aqua complex: A theoretical point of view

    Journal of Physical Chemistry B, Vol. 114, Núm. 25, pp. 8525-8535

2009

  1. Molecular dynamics and quantum mechanical calculations on the mononuclear zinc-β-lactamase from Bacillus cereus: Protonation state of the active site and imipenem binding

    Journal of Molecular Structure: THEOCHEM, Vol. 912, Núm. 1-3, pp. 105-112

  2. Thermochemical fragment energy method for biomolecules: Application to a collagen model peptide

    Journal of Chemical Theory and Computation, Vol. 5, Núm. 6, pp. 1667-1679

2008

  1. Entropic control of the relative stability of triple-helical collagen peptide models

    Journal of Physical Chemistry B, Vol. 112, Núm. 47, pp. 15248-15255

  2. From the X-ray compact structure to the elongated form of the full-length MMP-2 enzyme in solution: A molecular dynamics study

    Journal of the American Chemical Society, Vol. 130, Núm. 43, pp. 14070-14071

  3. Peptide hydrolysis catalyzed by matrix metalloproteinase 2: A computational study

    Journal of Physical Chemistry B, Vol. 112, Núm. 28, pp. 8412-8424

2007

  1. Molecular dynamics simulations of matrix metalloproteinase 2: Role of the structural metal ions

    Biochemistry, Vol. 46, Núm. 31, pp. 8943-8952

2006

  1. A computational study of the deacylation mechanism of human butyrylcholinesterase

    Biochemistry, Vol. 45, Núm. 24, pp. 7529-7543

  2. Quantum chemical study on the coordination environment of the catalytic zinc ion in matrix metalloproteinases

    Journal of Physical Chemistry B, Vol. 110, Núm. 47, pp. 24222-24230

  3. Theoretical studies on the ring opening of β-lactams: Processes in solution and in enzymatic media

    Current Organic Chemistry, Vol. 10, Núm. 7, pp. 805-821

2005

  1. Insights into the base catalysis exerted by the DD-transpeptidase from Streptomyces K15: A molecular dynamics study

    Biochemistry, Vol. 44, Núm. 9, pp. 3225-3240

2001

  1. Evaluation of the catalytic mechanism of AICAR transformylase by pH-dependent kinetics, mutagenesis, and quantum chemical calculations

    Journal of the American Chemical Society, Vol. 123, Núm. 20, pp. 4687-4696

  2. Molecular dynamics study of the IIA binding site in human serum albumin: Influence of the protonation state of Lys195 and Lys199

    Journal of Medicinal Chemistry, Vol. 44, Núm. 2, pp. 250-260