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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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Elucidating the molecular logic of a metabotropic glutamate receptor heterodimer

Nature communications, 2024-10, Vol.15 (1), p.8552-15, Article 8552

2024

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Impact of Lipid Composition and Receptor Conformation on the Spatio-temporal Organization of μ-Opioid Receptors in a Multi-component Plasma Membrane Model

PLoS computational biology, 2016-12, Vol.12 (12), p.e1005240-e1005240

2016

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Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis

PLoS computational biology, 2019-01, Vol.15 (1), p.e1006689-e1006689

2019

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Preferred supramolecular organization and dimer interfaces of opioid receptors from simulated self-association

PLoS computational biology, 2015-03, Vol.11 (3), p.e1004148-e1004148

2015

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Assessing the relative stability of dimer interfaces in g protein-coupled receptors

PLoS computational biology, 2012-08, Vol.8 (8), p.e1002649-e1002649

2012

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Differences in interactions between transmembrane domains tune the activation of metabotropic glutamate receptors

eLife, 2021-04, Vol.10

2021

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Proposed Mode of Binding and Action of Positive Allosteric Modulators at Opioid Receptors

ACS chemical biology, 2016-05, Vol.11 (5), p.1220-1229

2016

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Decoding the Signaling of a GPCR Heteromeric Complex Reveals a Unifying Mechanism of Action of Antipsychotic Drugs

Cell, 2011-11, Vol.147 (5), p.1011-1023

2011

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The Dynamic Process of Drug-GPCR Binding at Either Orthosteric or Allosteric Sites Evaluated by Metadynamics

Methods in molecular biology (Clifton, N.J.), 2015, Vol.1335, p.277

2015

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Ligand-induced modulation of the free-energy landscape of G protein-coupled receptors explored by adaptive biasing techniques

PLoS computational biology, 2011-10, Vol.7 (10), p.e1002193-e1002193

2011

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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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Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy

Proceedings of the National Academy of Sciences - PNAS, 2013-02, Vol.110 (6), p.2140-2145

2013

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Transfer learning of deep hybrid ligand-based and structure-based drug discovery schemes for improved prediction of opioid ligands’ bioactivity

Biophysical journal, 2024-02, Vol.123 (3), p.428a-428a

2024

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Ligand-Binding Calculations with Metadynamics

Methods in molecular biology (Clifton, N.J.), 2019, Vol.2022, p.233

Provasi, Davide

2019

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Publisher Correction: GPCRmd uncovers the dynamics of the 3D-GPCRome

Nature methods, 2020-08, Vol.17 (8), p.861-862

2020

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Exploring the protein G helix free-energy surface by solute tempering metadynamics

Proteins, structure, function, and bioinformatics, 2008-06, Vol.71 (4), p.1647-1654

2008

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How Oliceridine (TRV-130) Binds and Stabilizes a μ‑Opioid Receptor Conformational State That Selectively Triggers G Protein Signaling Pathways

Biochemistry (Easton), 2016-11, Vol.55 (46), p.6456-6466

2016

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Gαs slow conformational transition upon GTP binding and a novel Gαs regulator

iScience, 2023-05, Vol.26 (5), p.106603, Article 106603

2023

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Molecular Determinants and Thermodynamics of the Amyloid Precursor Protein Transmembrane Domain Implicated in Alzheimer's Disease

Journal of molecular biology, 2011-05, Vol.408 (5), p.879-895

2011

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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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Computational structural biology of opioid receptors

Methods in molecular biology (Clifton, N.J.), 2015, Vol.1230, p.13

Provasi, Davide

2015

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Targeted molecular dynamics reveals overall common conformational changes upon hybrid domain swing-out in β3 integrins

Proteins, structure, function, and bioinformatics, 2009-11, Vol.77 (2), p.477-489

2009

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Atomic-Level Characterization of the Methadone-Stabilized Active Conformation of µ -Opioid Receptor

Molecular pharmacology, 2020-10, Vol.98 (4), p.475-486

2020

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Putative Active States of a Prototypic G-Protein-Coupled Receptor from Biased Molecular Dynamics

Biophysical journal, 2010-05, Vol.98 (10), p.2347-2355

2010

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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

Elucidating the molecular logic of a metabotropic glutamate receptor heterodimer

Impact of Lipid Composition and Receptor Conformation on the Spatio-temporal Organization of μ-Opioid Receptors in a Multi-component Plasma Membrane Model

Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis

Preferred supramolecular organization and dimer interfaces of opioid receptors from simulated self-association

Assessing the relative stability of dimer interfaces in g protein-coupled receptors

Differences in interactions between transmembrane domains tune the activation of metabotropic glutamate receptors

Proposed Mode of Binding and Action of Positive Allosteric Modulators at Opioid Receptors

Decoding the Signaling of a GPCR Heteromeric Complex Reveals a Unifying Mechanism of Action of Antipsychotic Drugs

The Dynamic Process of Drug-GPCR Binding at Either Orthosteric or Allosteric Sites Evaluated by Metadynamics

Ligand-induced modulation of the free-energy landscape of G protein-coupled receptors explored by adaptive biasing techniques

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

Inward-facing conformation of the zinc transporter YiiP revealed by cryoelectron microscopy

Transfer learning of deep hybrid ligand-based and structure-based drug discovery schemes for improved prediction of opioid ligands’ bioactivity

Ligand-Binding Calculations with Metadynamics

Publisher Correction: GPCRmd uncovers the dynamics of the 3D-GPCRome

Exploring the protein G helix free-energy surface by solute tempering metadynamics

How Oliceridine (TRV-130) Binds and Stabilizes a μ‑Opioid Receptor Conformational State That Selectively Triggers G Protein Signaling Pathways

Gαs slow conformational transition upon GTP binding and a novel Gαs regulator

Molecular Determinants and Thermodynamics of the Amyloid Precursor Protein Transmembrane Domain Implicated in Alzheimer's Disease

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

Computational structural biology of opioid receptors

Targeted molecular dynamics reveals overall common conformational changes upon hybrid domain swing-out in β3 integrins

Atomic-Level Characterization of the Methadone-Stabilized Active Conformation of µ -Opioid Receptor

Putative Active States of a Prototypic G-Protein-Coupled Receptor from Biased Molecular Dynamics

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