Lista de obras - Francesca Spyrakis - Dominio Público Uruguay

4-Amino-1,2,4-triazole-3-thione as a Promising Scaffold for the Inhibition of Serine and Metallo-β-Lactamases

scientific article published on 24 March 2020

A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins.

artículo científico publicado en 2015

A novel Bim-BH3-derived Bcl-XL inhibitor: biochemical characterization, in vitro, in vivo and ex-vivo anti-leukemic activity

artículo científico publicado en 2008

Allosteric communication between alpha and beta subunits of tryptophan synthase: modelling the open-closed transition of the alpha subunit

artículo científico publicado en 2006

BioGPS: The Music for the Chemo- and Bioinformatics Walzer

artículo científico publicado en 2014

Bound water at protein-protein interfaces: partners, roles and hydrophobic bubbles as a conserved motif

artículo científico publicado en 2011

CO Rebinding Kinetics and Molecular Dynamics Simulations Highlight Dynamic Regulation of Internal Cavities in Human Cytoglobin

artículo científico publicado en 2013

Can We Exploit β-Lactamases Intrinsic Dynamics for Designing More Effective Inhibitors?

artículo científico publicado en 2020

Chemogenomics of pyridoxal 5'-phosphate dependent enzymes

artículo científico publicado en 2011

Comparing Drug Images and Repurposing Drugs with BioGPS and FLAPdock: The Thymidylate Synthase Case.

artículo científico publicado en 2016

Complexity in modeling and understanding protonation states: computational titration of HIV-1-protease-inhibitor complexes

artículo científico publicado en 2007

Computational titration analysis of a multiprotic HIV-1 protease-ligand complex.

artículo científico publicado en 2004

Correct protonation states and relevant waters = better computational simulations?

artículo científico

Correction: Recent advances in the synthesis of analogues of phytohormones strigolactones with ring-closing metathesis as a key step

artículo científico publicado en 2017

Cryo-EM structures of staphylococcal IsdB bound to human hemoglobin reveal the process of heme extraction

scientific article published on 31 March 2022

Design of O -Acetylserine Sulfhydrylase Inhibitors by Mimicking Nature

artículo científico publicado en 2010

Different roles of protein dynamics and ligand migration in non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana

article

Discovering New Casein Kinase 1d Inhibitors with an Innovative Molecular Dynamics Enabled Virtual Screening Workflow

scientific article published on 13 December 2018

Energetics of the protein-DNA-water interaction

artículo científico publicado en 2007

Energy-based prediction of amino acid-nucleotide base recognition

artículo científico publicado en 2008

Expanding the chemical space of human serine racemase inhibitors

artículo científico publicado en 2015

FADB: a food additive molecular database for in silico screening in food toxicology

artículo científico publicado en 2014

Fine tuning of the active site modulates specificity in the interaction of O-acetylserine sulfhydrylase isozymes with serine acetyltransferase

artículo científico publicado en 2012

First virtual screening and experimental validation of inhibitors targeting GES-5 carbapenemase

scientific article published on 02 January 2019

Folic Acid-Peptide Conjugates Combine Selective Cancer Cell Internalization with Thymidylate Synthase Dimer Interface Targeting

artículo científico publicado en 2021

From Experiments to a Fast Easy-to-Use Computational Methodology to Predict Human Aldehyde Oxidase Selectivity and Metabolic Reactions.

artículo científico publicado en 2017

Geminate rebinding in R-state hemoglobin: kinetic and computational evidence for multiple hydrophobic pockets

artículo científico publicado en 2005

Getting it right: modeling of pH, solvent and "nearly" everything else in virtual screening of biological targets

artículo científico publicado en 2004

Histidine E7 Dynamics Modulates Ligand Exchange between Distal Pocket and Solvent in AHb1 fromArabidopsis thaliana

artículo científico publicado en 2011

How computational methods try to disclose the estrogen receptor secrecy--modeling the flexibility.

artículo científico publicado en 2009

Interaction of human hemoglobin and semi-hemoglobins with the Staphylococcus aureus hemophore IsdB: a kinetic and mechanistic insight

artículo científico publicado en 2019

Iron Metabolism at the Interface between Host and Pathogen: From Nutritional Immunity to Antibacterial Development

artículo científico publicado en 2020

Isozyme-specific ligands for O-acetylserine sulfhydrylase, a novel antibiotic target

artículo científico publicado en 2013

Ligand migration and hexacoordination in type 1 non-symbiotic rice hemoglobin

artículo científico publicado en 2010

Ligand migration in nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana

artículo científico publicado en 2007

Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations.

artículo científico publicado en 2013

Ligand migration through the internal hydrophobic cavities in human neuroglobin

artículo científico publicado en 2009

Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules

artículo científico publicado en 2006

Modulating Ligand Dissociation through Methyl Isomerism in Accessory Sites: Binding of Retinol to Cellular Carriers

scientific article published on 14 November 2019

NO release regulated by doxorubicin as the green light-harvesting antenna

scientific article published on 21 May 2020

Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description.

artículo científico

Oxygen and nitric oxide rebinding kinetics in nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana

artículo científico publicado en 2011

Oxygen binding to Arabidopsis thaliana AHb2 nonsymbiotic hemoglobin: evidence for a role in oxygen transport

article

Paracetamol-Galactose Conjugate: A Novel Prodrug for an Old Analgesic Drug

artículo científico publicado en 2019

Rational Design of a User-Friendly Aptamer/Peptide-Based Device for the Detection of Staphylococcus aureus

artículo científico publicado en 2020

Recent advances in the synthesis of analogues of phytohormones strigolactones with ring-closing metathesis as a key step

artículo científico publicado en 2017

Robust Classification of “Relevant” Water Molecules in Putative Protein Binding Sites

scientific article published on 31 January 2008

Serine racemase: a key player in neuron activity and in neuropathologies

artículo científico publicado en 2013

Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 3. The Free Energy Contribution of Structural Water Molecules in HIV-1 Protease Complexes

article

Strigolactone Analogs Are Promising Antiviral Agents for the Treatment of Human Cytomegalovirus Infection

scientific article published on 10 May 2020

Structural insight into the interaction of O-acetylserine sulfhydrylase with competitive, peptidic inhibitors by saturation transfer difference-NMR.

artículo científico publicado en 2016

Structural plasticity and functional implications of internal cavities in distal mutants of type 1 non-symbiotic hemoglobin AHb1 from Arabidopsis thaliana.

artículo científico publicado en 2009

Structure-Based Virtual Screening for the Discovery of Novel Inhibitors of New Delhi Metallo-β-lactamase-1.

artículo científico publicado en 2017

Structure-activity relationships of strigolactones via a novel, quantitative in planta bioassay.

artículo científico publicado en 2018

Target flexibility: an emerging consideration in drug discovery and design

scientific article published on 12 September 2008

Targeting cystalysin, a virulence factor of treponema denticola-supported periodontitis

artículo científico publicado en 2014

Ten Years with New Delhi Metallo-β-lactamase-1 (NDM-1): From Structural Insights to Inhibitor Design

scientific article published on 28 November 2018

The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery.

artículo científico publicado en 2017

The consequences of scoring docked ligand conformations using free energy correlations

artículo científico publicado en 2007

The inhibition of extended spectrum β-lactamases: hits and leads

artículo científico publicado en 2014

The multifaceted pyridoxal 5'-phosphate-dependent O-acetylserine sulfhydrylase

artículo científico publicado en 2011

The reactivity with CO of AHb1 and AHb2 from Arabidopsis thaliana is controlled by the distal HisE7 and internal hydrophobic cavities

artículo científico publicado en 2007

Tools for building a comprehensive modeling system for virtual screening under real biological conditions: The Computational Titration algorithm

artículo científico publicado en 2005

Tuning the Hydrophobicity of a Mitochondria-Targeted NO Photodonor

artículo científico publicado en 2018

Unintended consequences? Water molecules at biological and crystallographic protein-protein interfaces

artículo científico publicado en 2013

Water: How to evaluate its contribution in protein-ligand interactions

article by Pietro Cozzini et al published 2005 in International Journal of Quantum Chemistry

Lista de obras de Francesca Spyrakis

4-Amino-1,2,4-triazole-3-thione as a Promising Scaffold for the Inhibition of Serine and Metallo-β-Lactamases

A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins.

A novel Bim-BH3-derived Bcl-XL inhibitor: biochemical characterization, in vitro, in vivo and ex-vivo anti-leukemic activity

Allosteric communication between alpha and beta subunits of tryptophan synthase: modelling the open-closed transition of the alpha subunit

BioGPS: The Music for the Chemo- and Bioinformatics Walzer

Bound water at protein-protein interfaces: partners, roles and hydrophobic bubbles as a conserved motif

CO Rebinding Kinetics and Molecular Dynamics Simulations Highlight Dynamic Regulation of Internal Cavities in Human Cytoglobin

Can We Exploit β-Lactamases Intrinsic Dynamics for Designing More Effective Inhibitors?

Chemogenomics of pyridoxal 5'-phosphate dependent enzymes

Comparing Drug Images and Repurposing Drugs with BioGPS and FLAPdock: The Thymidylate Synthase Case.

Complexity in modeling and understanding protonation states: computational titration of HIV-1-protease-inhibitor complexes

Computational titration analysis of a multiprotic HIV-1 protease-ligand complex.

Correct protonation states and relevant waters = better computational simulations?

Correction: Recent advances in the synthesis of analogues of phytohormones strigolactones with ring-closing metathesis as a key step

Cryo-EM structures of staphylococcal IsdB bound to human hemoglobin reveal the process of heme extraction

Design of O -Acetylserine Sulfhydrylase Inhibitors by Mimicking Nature

Different roles of protein dynamics and ligand migration in non-symbiotic hemoglobins AHb1 and AHb2 from Arabidopsis thaliana

Discovering New Casein Kinase 1d Inhibitors with an Innovative Molecular Dynamics Enabled Virtual Screening Workflow

Energetics of the protein-DNA-water interaction

Energy-based prediction of amino acid-nucleotide base recognition

Expanding the chemical space of human serine racemase inhibitors

FADB: a food additive molecular database for in silico screening in food toxicology

Fine tuning of the active site modulates specificity in the interaction of O-acetylserine sulfhydrylase isozymes with serine acetyltransferase

First virtual screening and experimental validation of inhibitors targeting GES-5 carbapenemase

Folic Acid-Peptide Conjugates Combine Selective Cancer Cell Internalization with Thymidylate Synthase Dimer Interface Targeting

From Experiments to a Fast Easy-to-Use Computational Methodology to Predict Human Aldehyde Oxidase Selectivity and Metabolic Reactions.

Geminate rebinding in R-state hemoglobin: kinetic and computational evidence for multiple hydrophobic pockets

Getting it right: modeling of pH, solvent and "nearly" everything else in virtual screening of biological targets

Histidine E7 Dynamics Modulates Ligand Exchange between Distal Pocket and Solvent in AHb1 fromArabidopsis thaliana

How computational methods try to disclose the estrogen receptor secrecy--modeling the flexibility.

Interaction of human hemoglobin and semi-hemoglobins with the Staphylococcus aureus hemophore IsdB: a kinetic and mechanistic insight

Iron Metabolism at the Interface between Host and Pathogen: From Nutritional Immunity to Antibacterial Development

Isozyme-specific ligands for O-acetylserine sulfhydrylase, a novel antibiotic target

Ligand migration and hexacoordination in type 1 non-symbiotic rice hemoglobin

Ligand migration in nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana

Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations.

Ligand migration through the internal hydrophobic cavities in human neuroglobin

Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: predictive tools for characterizing the roles of water in biomolecules

Modulating Ligand Dissociation through Methyl Isomerism in Accessory Sites: Binding of Retinol to Cellular Carriers

NO release regulated by doxorubicin as the green light-harvesting antenna

Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description.

Oxygen and nitric oxide rebinding kinetics in nonsymbiotic hemoglobin AHb1 from Arabidopsis thaliana

Oxygen binding to Arabidopsis thaliana AHb2 nonsymbiotic hemoglobin: evidence for a role in oxygen transport

Paracetamol-Galactose Conjugate: A Novel Prodrug for an Old Analgesic Drug

Rational Design of a User-Friendly Aptamer/Peptide-Based Device for the Detection of Staphylococcus aureus

Recent advances in the synthesis of analogues of phytohormones strigolactones with ring-closing metathesis as a key step

Robust Classification of “Relevant” Water Molecules in Putative Protein Binding Sites

Serine racemase: a key player in neuron activity and in neuropathologies

Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 3. The Free Energy Contribution of Structural Water Molecules in HIV-1 Protease Complexes

Strigolactone Analogs Are Promising Antiviral Agents for the Treatment of Human Cytomegalovirus Infection

Structural insight into the interaction of O-acetylserine sulfhydrylase with competitive, peptidic inhibitors by saturation transfer difference-NMR.

Structural plasticity and functional implications of internal cavities in distal mutants of type 1 non-symbiotic hemoglobin AHb1 from Arabidopsis thaliana.

Structure-Based Virtual Screening for the Discovery of Novel Inhibitors of New Delhi Metallo-β-lactamase-1.

Structure-activity relationships of strigolactones via a novel, quantitative in planta bioassay.

Target flexibility: an emerging consideration in drug discovery and design

Targeting cystalysin, a virulence factor of treponema denticola-supported periodontitis

Ten Years with New Delhi Metallo-β-lactamase-1 (NDM-1): From Structural Insights to Inhibitor Design

The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery.

The consequences of scoring docked ligand conformations using free energy correlations

The inhibition of extended spectrum β-lactamases: hits and leads

The multifaceted pyridoxal 5'-phosphate-dependent O-acetylserine sulfhydrylase

The reactivity with CO of AHb1 and AHb2 from Arabidopsis thaliana is controlled by the distal HisE7 and internal hydrophobic cavities

Tools for building a comprehensive modeling system for virtual screening under real biological conditions: The Computational Titration algorithm

Tuning the Hydrophobicity of a Mitochondria-Targeted NO Photodonor

Unintended consequences? Water molecules at biological and crystallographic protein-protein interfaces

Water: How to evaluate its contribution in protein-ligand interactions