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Synthetic and Receptor Signaling Explorations of the Mitragyna Alkaloids: Mitragynine as an Atypical Molecular Framework for Opioid Receptor Modulators

Journal of the American Chemical Society, 2016-06, Vol.138 (21), p.6754-6764

2016

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A combination of machine learning and infrequent metadynamics to efficiently predict kinetic rates, transition states, and molecular determinants of drug dissociation from G protein-coupled receptors

The Journal of chemical physics, 2020-09, Vol.153 (12), p.124105-124105

2020

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Differential stability of the crystallographic interfaces of mu- and kappa-opioid receptors

PloS one, 2014-02, Vol.9 (2), p.e90694-e90694

2014

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Enhancing Opioid Bioactivity Predictions through Integration of Ligand-Based and Structure-Based Drug Discovery Strategies with Transfer and Deep Learning Techniques

The journal of physical chemistry. B, 2023-12, Vol.127 (50), p.10691-10699

2023

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G Protein-Coupled Receptors - Modeling and Simulation

Filizola, Marta

2014, 2013

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Phosphorylation of the retinoic acid receptor alpha induces a mechanical allosteric regulation and changes in internal dynamics

PLoS computational biology, 2013-04, Vol.9 (4), p.e1003012-e1003012

2013

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An efficient strategy to estimate thermodynamics and kinetics of G protein-coupled receptor activation using metadynamics and maximum caliber

The Journal of chemical physics, 2018-12, Vol.149 (22), p.224101-224101

2018

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De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework

Journal of chemical information and modeling, 2023-08, Vol.63 (16), p.5056-5065

2023

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Discovery of a Novel Selective Kappa-Opioid Receptor Agonist Using Crystal Structure-Based Virtual Screening

Journal of chemical information and modeling, 2013-03, Vol.53 (3), p.521-526

2013

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Ligand-Based Discovery of a New Scaffold for Allosteric Modulation of the μ‑Opioid Receptor

Journal of chemical information and modeling, 2015-09, Vol.55 (9), p.1836-1843

2015

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A novel class of ion displacement ligands as antagonists of the alpha IIb beta 3 receptor that limit conformational reorganization of the receptor

Bioorganic & medicinal chemistry letters, 2014-02, Vol.24 (4), p.1148-1153

2014

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Structure-based virtual screening of small-molecule antagonists of platelet integrin αIIbβ3 that do not prime the receptor to bind ligand

Journal of computer-aided molecular design, 2012-09, Vol.26 (9), p.1005-1015

2012

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Role of Protein Environment in Horseradish Peroxidase Compound I Formation: Molecular Dynamics Simulations of Horseradish Peroxidase−HOOH Complex

Journal of the American Chemical Society, 2000-01, Vol.122 (1), p.18-25

2000

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Amygdalin binds to the CD4 receptor as suggested from molecular modeling studies

Bioorganic & medicinal chemistry letters, 1998-04, Vol.8 (7), p.781-786

1998

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Molecular determinants of non-specific recognition of δ, μ, and κ opioid receptors

Bioorganic & medicinal chemistry, 2001, Vol.9 (1), p.69-76

2001

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Probing the Role of Protein Environment in Compound I Formation of Chloroperoxidase (CPO)

Journal of the American Chemical Society, 2000-04, Vol.122 (15), p.3599-3605

2000

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Evaluation of the iterative simulated annealing technique in conformational search of peptides

Chemical physics letters, 2000-03, Vol.319 (1), p.65-70

2000

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Molecular determinants of recognition and activation at GABA A /benzodiazepine receptors

International journal of quantum chemistry, 2002-05, Vol.88 (1), p.56-64

2002

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Global physicochemical properties as activity discriminants for the mGluR1 subtype of metabotropic glutamate receptors

Journal of computational chemistry, 2001-12, Vol.22 (16), p.2018-2027

2001

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Assessment of the bioactive conformation of the vasoactive intestinal peptide by computational methods

International journal of quantum chemistry, 2002, Vol.88 (1), p.201-210

2002

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Modeling the 3D Structure of Rhodopsin Using a De Novo Approach to Build G-protein−Coupled Receptors

The journal of physical chemistry. B, 1999-04, Vol.103 (13), p.2520-2527

1999

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Differentiation of [delta], [mu], and [kappa] opioid receptor agonists based on pharmacophore development and computed physicochemical properties

Journal of computer-aided molecular design, 2001-04, Vol.15 (4), p.297

2001

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New insights into the conformational requirements of B2 bradykinin antagonism

Bioorganic & medicinal chemistry, 1998-09, Vol.6 (9), p.1491-1500

1998

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Synthetic and Receptor Signaling Explorations of the Mitragyna Alkaloids: Mitragynine as an Atypical Molecular Framework for Opioid Receptor Modulators

A combination of machine learning and infrequent metadynamics to efficiently predict kinetic rates, transition states, and molecular determinants of drug dissociation from G protein-coupled receptors

Differential stability of the crystallographic interfaces of mu- and kappa-opioid receptors

Enhancing Opioid Bioactivity Predictions through Integration of Ligand-Based and Structure-Based Drug Discovery Strategies with Transfer and Deep Learning Techniques

G Protein-Coupled Receptors - Modeling and Simulation

Phosphorylation of the retinoic acid receptor alpha induces a mechanical allosteric regulation and changes in internal dynamics

An efficient strategy to estimate thermodynamics and kinetics of G protein-coupled receptor activation using metadynamics and maximum caliber

De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework

Discovery of a Novel Selective Kappa-Opioid Receptor Agonist Using Crystal Structure-Based Virtual Screening

Ligand-Based Discovery of a New Scaffold for Allosteric Modulation of the μ‑Opioid Receptor

A novel class of ion displacement ligands as antagonists of the alpha IIb beta 3 receptor that limit conformational reorganization of the receptor

Structure-based virtual screening of small-molecule antagonists of platelet integrin αIIbβ3 that do not prime the receptor to bind ligand

Role of Protein Environment in Horseradish Peroxidase Compound I Formation: Molecular Dynamics Simulations of Horseradish Peroxidase−HOOH Complex

Amygdalin binds to the CD4 receptor as suggested from molecular modeling studies

Molecular determinants of non-specific recognition of δ, μ, and κ opioid receptors

Probing the Role of Protein Environment in Compound I Formation of Chloroperoxidase (CPO)

Evaluation of the iterative simulated annealing technique in conformational search of peptides

Molecular determinants of recognition and activation at GABA A /benzodiazepine receptors

Global physicochemical properties as activity discriminants for the mGluR1 subtype of metabotropic glutamate receptors

Assessment of the bioactive conformation of the vasoactive intestinal peptide by computational methods

Modeling the 3D Structure of Rhodopsin Using a De Novo Approach to Build G-protein−Coupled Receptors

Differentiation of [delta], [mu], and [kappa] opioid receptor agonists based on pharmacophore development and computed physicochemical properties

New insights into the conformational requirements of B2 bradykinin antagonism

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