Natalia Díaz

Latest

Assessment of Energy Effects Determining cis-trans Proline Isomerization in Dipeptides
Disposable electrochemical aptasensor for rapid and selective vancomycin detection in clinical samples: Bridging affinity selection, computational modeling and clinical validation
Refinement and Truncation of DNA Aptamers Based on Molecular Dynamics Simulations: Computational Protocol and Experimental Validation
Assessing the Interactions between Snake Venom Metalloproteinases and Hydroxamate Inhibitors Using Kinetic and ITC Assays, Molecular Dynamics Simulations and MM/PBSA-Based Scoring Functions
Atoms in molecules in real space: a fertile field for chemical bonding
Amphiphilic cyclodextrins: Dimerization and diazepam binding explored by molecular dynamics simulations
QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach
Toward Reliable and Insightful Entropy Calculations on Flexible Molecules
Influence of charge configuration on substrate binding to SARS-CoV-2 main protease
Understanding the Conformational Properties of Fluorinated Polypeptides: Molecular Modelling of Unguisin A
Alkali and Alkaline-Earth Cations in Complexes with Small Bioorganic Ligands: Ab Initio Benchmark Calculations and Bond Energy Decomposition
Aptamers targeting protein-specific glycosylation in tumor biomarkers: general selection, characterization and structural modeling
SARS-CoV-2 Main Protease: A Molecular Dynamic Study
SARS-CoV-2 Main Protease: A Molecular Dynamics Study
Affinity Calculations of Cyclodextrin Host–Guest Complexes: Assessment of Strengths and Weaknesses of End-Point Free Energy Methods
Fluorine conformational effects characterized by energy decomposition analysis
Application of the Interacting Quantum Atoms Approach to the S66 and Ionic-HB Datasets for Noncovalent Interactions.
Interacting Quantum Atoms Approach and Electrostatic Solvation Energy: Assessing Atomic and Group Solvation Contributions
Conformational and entropy analyses of extended molecular dynamics simulations of α-, β- and γ-cyclodextrins and of the β-cyclodextrin/nabumetone complex
Ligand Strain and Entropic Effects on the Binding of Macrocyclic and Linear Inhibitors: Molecular Modeling of Penicillopepsin Complexes
Molecular dynamics studies of matrix metalloproteases
Role of the Protonation State on the Structure and Dynamics of Albumin
Unraveling the distinctive features of hemorrhagic and non-hemorrhagic snake venom metalloproteinases using molecular simulations
Direct methods for computing single-molecule entropies from molecular simulations
Extensive Simulations of the Full-Length Matrix Metalloproteinase-2 Enzyme in a Prereactive Complex with a Collagen Triple-Helical Peptide
Molecular Modeling of Bioorganometallic Compounds: Thermodynamic Properties of Molybdocene-Glutathione Complexes and Mechanism of Peptide Hydrolysis
A Combined Semiempirical and DFT Computational Protocol for Studying Bioorganometallic Complexes: Application to Molybdocene-Cysteine Complexes
An Integrated Computational and Experimental Approach to Gaining Selectivity for MMP-2 within the Gelatinase Subfamily
Sampling Assessment for Molecular Simulations Using Conformational Entropy Calculations
CENCALC: A Computational Tool for Conformational Entropy Calculations from Molecular Simulations
Progress towards water-soluble triazole-based selective MMP-2 inhibitors
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
Alternative Interdomain Configurations of the Full-Length MMP-2 Enzyme Explored by Molecular Dynamics Simulations
Ab Initio Benchmark Calculations on Ca(II) Complexes and Assessment of Density Functional Theory Methodologies
Entropy Calculations of Single Molecules by Combining the Rigid-Rotor and Harmonic-Oscillator Approximations with Conformational Entropy Estimations from Molecular Dynamics Simulations
Quantum chemical calculations of stability constants: study of ligand effects on the relative stability of Pd(II)-peptide complexes
Interdomain Conformations in the Full-Length MMP-2 Enzyme Explored by Protein-Protein Docking Calculations Using pyDock
Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: Molecular dynamics and QM/MM calculations
Understanding Regioselective Cleavage in Peptide Hydrolysis by a Palladium(II) Aqua Complex: A Theoretical Point of View
Molecular dynamics and quantum mechanical calculations on the mononuclear zinc-beta-lactamase from Bacillus cereus: Protonation state of the active site and imipenem binding
Thermochemical Fragment Energy Method for Biomolecules: Application to a Collagen Model Peptide
Entropic Control of the Relative Stability of Triple-helical Collagen Peptide Models
From the X-ray Compact Structure to the Elongated Form of the Full-Length MMP-2 Enzyme in Solution: A Molecular Dynamics Study
Molecular dynamics simulations of the active matrix metalloproteinase-2: Positioning of the N-terminal fragment and binding of a small peptide substrate
Monoligand Zn(II) complexes: Ab initio benchmark calculations and comparison with density functional theory methodologies
Ring opening at N1-C2 bond of azetidin-2-ones by a molybdenum hydroxo-carbonyl complex: evidence from a computational study
Molecular dynamics simulations of matrix metalloproteinase 2: Role of the structural metal ions
A computational study of the deacylation mechanism of human butyrylcholinesterase
Assessing the protonation state of drug molecules: The case of aztreonam
Molecular dynamics simulations of class C beta-lactamase from Citrobacter freundii: Insights into the base catalyst for acylation
Quantum chemical study on the coordination environment of the catalytic zinc ion in matrix metalloproteinases
Insights into the base catalysis exerted by the DD-transpeptidase from Streptomyces K15: A molecular dynamics study
Molecular dynamics simulations of the TEM-1,beta-lactamase complexed with cephalothin
Insights into the phosphoryl-transfer mechanism of cAMP-dependent protein kinase from quantum chemical calculations and molecular dynamics simulations
Zn2+ catalysed hydrolysis of beta-lactams: experimental and theoretical studies on the influence of the beta-lactam structure
A combined theoretical and experimental research project into the aminolysis of beta-lactam antibiotics: The importance of bifunctional catalysis
Conformational properties of penicillins: Quantum chemical calculations and molecular dynamics simulations of benzylpenicillin
Insights into the acylation mechanism of class A beta-lactamases from molecular dynamics simulations of the TEM-1 enzyme complexed with benzylpenicillin
Ureases: Quantum chemical calculations on cluster models
Molecular dynamics simulations of the dinuclear zinc-beta-lactamase from bacteroides fragilis complexed with imipenem
Theoretical study of ammonolysis of monobactams: Kinetic role of the N-sulfonate group
Water-assisted alkaline hydrolysis of monobactams: A theoretical study
A theoretical study of the aminolysis reaction of lysine 199 of human serum albumin with benzylpenicillin: Consequences for immunochemistry of penicillins
Acylation of class a beta-lactamases by penicillins: A theoretical examination of the role of serine 130 and the beta-lactam carboxylate group
Evaluation of the catalytic mechanism of AICAR transformylase by pH-dependent kinetics, mutagenesis, and quantum chemical calculations
Molecular dynamics study of the IIA binding site in human serum albumin: Influence of the protonation state of Lys195 and Lys199
Hydration of zinc ions: theoretical study of [Zn(H2O)(4)](H2O)(8)(2+) and [Zn(H2O)(6)](H2O)(6)(2+)
Theoretical study of the water-assisted aminolysis of beta-lactams: Implications for the reaction between human serum albumin and penicillins
Zinc metallo-beta-lactamase from Bacteroides fragilis: A quantum chemical study on model systems of the active site
Ammonolysis and aminolysis of beta-lactams: A theoretical study
Importance of a synperiplanar stepwise mechanism through neutral intermediates in the aminolysis of monocyclic beta-lactams: A theoretical analysis
NH3-assisted ammonolysis of beta-lactams: A theoretical study
Theoretical study of the reaction (1)[: CH2]+CHO+-> CH3++CO