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Best Practices on QM/MM Simulations of Biological Systems

Journal of chemical information and modeling, 2023-05, Vol.63 (9), p.2609-2627

2023

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Molecular Dynamics in Mixed Solvents Reveals Protein–Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions

Journal of chemical information and modeling, 2017-04, Vol.57 (4), p.846-863

2017

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Reactions of HNO with Metal Porphyrins: Underscoring the Biological Relevance of HNO

Accounts of chemical research, 2014-10, Vol.47 (10), p.2907-2916

2014

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Evolutionary and Functional Relationships in the Truncated Hemoglobin Family

PLoS computational biology, 2016-01, Vol.12 (1), p.e1004701-e1004701

2016

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Unlocking Precision Docking for Metalloproteins

Journal of chemical information and modeling, 2024-03, Vol.64 (5), p.1581-1592

2024

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Globin phylogeny, evolution and function, the newest update

Proteins, structure, function, and bioinformatics, 2024-06, Vol.92 (6), p.720-734

2024

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Time-Resolved Electrochemical Quantification of Azanone (HNO) at Low Nanomolar Level

Analytical chemistry (Washington), 2013-11, Vol.85 (21), p.10262-10269

2013

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pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4

PLoS computational biology, 2012-11, Vol.8 (11), p.e1002761

2012

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H2S and NO cooperatively regulate vascular tone by activating a neuroendocrine HNO-TRPA1-CGRP signalling pathway

Nature communications, 2014-07, Vol.5 (1), p.4381, Article 4381

2014

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Nitric Oxide Is Reduced to HNO by Proton-Coupled Nucleophilic Attack by Ascorbate, Tyrosine, and Other Alcohols. A New Route to HNO in Biological Media?

Journal of the American Chemical Society, 2015-04, Vol.137 (14), p.4720-4727

2015

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The Structural Biology of Galectin-Ligand Recognition: Current Advances in Modeling Tools, Protein Engineering, and Inhibitor Design

Frontiers in chemistry, 2019-12, Vol.7, p.823-823

2019

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Tertiary and quaternary structural basis of oxygen affinity in human hemoglobin as revealed by multiscale simulations

Scientific reports, 2017-09, Vol.7 (1), p.10926-10, Article 10926

2017

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Rapid Whole-Cell Assay of Antitubercular Drugs Using Second-Generation Fluoromycobacteriophages

Antimicrobial agents and chemotherapy, 2016-05, Vol.60 (5), p.3253-3256

2016

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Mechanism of the Reaction of Human Manganese Superoxide Dismutase with Peroxynitrite: Nitration of Critical Tyrosine 34

Biochemistry (Easton), 2016-06, Vol.55 (24), p.3403-3417

2016

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A Novel SLC5A5 Variant Reveals the Crucial Role of Kinesin Light Chain 2 in Thyroid Hormonogenesis

The journal of clinical endocrinology and metabolism, 2021-07, Vol.106 (7), p.1867-1881

2021

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The Underlying Mechanism of HNO Production by the Myoglobin-Mediated Oxidation of Hydroxylamine

Inorganic chemistry, 2020-06, Vol.59 (12), p.7939-7952

2020

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Identification of novel molecular determinants of co-receptor usage in HIV-1 subtype F V3 envelope sequences

Scientific reports, 2020-07, Vol.10 (1), p.12583-12583, Article 12583

2020

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Redox Potential Determines the Reaction Mechanism of HNO Donors with Mn and Fe Porphyrins: Defining the Better Traps

Inorganic chemistry, 2014-07, Vol.53 (14), p.7351-7360

2014

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Trapping and Characterization of a Reaction Intermediate in Carbapenem Hydrolysis by B. cereus Metallo-β-lactamase

Journal of the American Chemical Society, 2008-11, Vol.130 (47), p.15852-15863

2008

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The Catalytic Mechanism of Peptidylglycine α-Hydroxylating Monooxygenase Investigated by Computer Simulation

Journal of the American Chemical Society, 2006-10, Vol.128 (39), p.12817-12828

2006

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The interplay between serine proteases and caspase-1 regulates the autophagy-mediated secretion of Interleukin-1 beta in human neutrophils

Frontiers in immunology, 2022-08, Vol.13, p.832306-832306

2022

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Evaluation of nitroxyl donors' effect on mycobacteria

Tuberculosis (Edinburgh, Scotland), 2018-03, Vol.109, p.35-40

2018

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From Genome to Drugs: New Approaches in Antimicrobial Discovery

Frontiers in pharmacology, 2021-06, Vol.12, p.647060-647060

2021

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A quantitative model for oxygen uptake and release in a family of hemeproteins

Bioinformatics, 2016-06, Vol.32 (12), p.1805-1813

2016

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Structure and function of crocodilian hemoglobins and allosteric regulation by chloride, ATP, and CO2

American journal of physiology. Regulatory, integrative and comparative physiology, 2020-03, Vol.318 (3), p.R657-R667

2020

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Best Practices on QM/MM Simulations of Biological Systems

Molecular Dynamics in Mixed Solvents Reveals Protein–Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions

Reactions of HNO with Metal Porphyrins: Underscoring the Biological Relevance of HNO

Evolutionary and Functional Relationships in the Truncated Hemoglobin Family

Unlocking Precision Docking for Metalloproteins

Globin phylogeny, evolution and function, the newest update

Time-Resolved Electrochemical Quantification of Azanone (HNO) at Low Nanomolar Level

pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4

H2S and NO cooperatively regulate vascular tone by activating a neuroendocrine HNO-TRPA1-CGRP signalling pathway

Nitric Oxide Is Reduced to HNO by Proton-Coupled Nucleophilic Attack by Ascorbate, Tyrosine, and Other Alcohols. A New Route to HNO in Biological Media?

The Structural Biology of Galectin-Ligand Recognition: Current Advances in Modeling Tools, Protein Engineering, and Inhibitor Design

Tertiary and quaternary structural basis of oxygen affinity in human hemoglobin as revealed by multiscale simulations

Rapid Whole-Cell Assay of Antitubercular Drugs Using Second-Generation Fluoromycobacteriophages

Mechanism of the Reaction of Human Manganese Superoxide Dismutase with Peroxynitrite: Nitration of Critical Tyrosine 34

A Novel SLC5A5 Variant Reveals the Crucial Role of Kinesin Light Chain 2 in Thyroid Hormonogenesis

The Underlying Mechanism of HNO Production by the Myoglobin-Mediated Oxidation of Hydroxylamine

Identification of novel molecular determinants of co-receptor usage in HIV-1 subtype F V3 envelope sequences

Redox Potential Determines the Reaction Mechanism of HNO Donors with Mn and Fe Porphyrins: Defining the Better Traps

Trapping and Characterization of a Reaction Intermediate in Carbapenem Hydrolysis by B. cereus Metallo-β-lactamase

The Catalytic Mechanism of Peptidylglycine α-Hydroxylating Monooxygenase Investigated by Computer Simulation

The interplay between serine proteases and caspase-1 regulates the autophagy-mediated secretion of Interleukin-1 beta in human neutrophils

Evaluation of nitroxyl donors' effect on mycobacteria

From Genome to Drugs: New Approaches in Antimicrobial Discovery

A quantitative model for oxygen uptake and release in a family of hemeproteins

Structure and function of crocodilian hemoglobins and allosteric regulation by chloride, ATP, and CO2

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