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Disordered linkers in multidomain allosteric proteins: Entropic effect to favor the open state or enhanced local concentration to favor the closed state?

Protein science, 2018-09, Vol.27 (9), p.1600-1610

2018

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Molecular‐dynamics simulation methods for macromolecular crystallography

Acta crystallographica. Section D, Biological crystallography., 2023-01, Vol.79 (1), p.50-65

2023

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Molecular Modeling in Drug Design

2019

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Identification of a conserved 8 aa insert in the PIP5K protein in the Saccharomycetaceae family of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role

Proteins, structure, function, and bioinformatics, 2017-08, Vol.85 (8), p.1454-1467

2017

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Exploring ligand dynamics in protein crystal structures with ensemble refinement

Acta crystallographica. Section D, Biological crystallography., 2021-08, Vol.77 (8), p.1099-1115

2021

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Coarse-grained molecular dynamics simulations of protein-ligand binding

Journal of computational chemistry, 2014-09, Vol.35 (25), p.1835-1845

2014

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The putative role of some conserved water molecules in the structure and function of human transthyretin

Acta crystallographica. Section D, Biological crystallography., 2015-11, Vol.71 (11), p.2248-2266

2015

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Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods

Fuxreiter, Monika

1, 2014

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Atomic-level characterization of protein–protein association

Proceedings of the National Academy of Sciences - PNAS, 2019-03, Vol.116 (10), p.4244-4249

2019

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In silico structural characterization of Cytochrome c oxidase Subunit 1: A transmembrane protein from Aedes aegypti

Journal of vector borne diseases, 2021-04, Vol.58 (2), p.106-114

2021

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MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

Journal of computational chemistry, 2011-07, Vol.32 (10), p.2319-2327

2011

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Phytochemicals-based targeting RdRp and main protease of SARS-CoV-2 using docking and steered molecular dynamic simulation: A promising therapeutic approach for Tackling COVID-19

Computers in biology and medicine, 2022-06, Vol.145, p.105468-105468, Article 105468

2022

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How does binding of agonist ligands control intrinsic molecular dynamics in human NMDA receptors?

PloS one, 2018-08, Vol.13 (8), p.e0201234-e0201234

2018

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Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2376, p.399

2022

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Structural and Evolutionary Analysis Indicate That the SARS-CoV-2 Mpro Is a Challenging Target for Small-Molecule Inhibitor Design

International journal of molecular sciences, 2020-04, Vol.21 (9), p.3099

2020

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Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine–lysine distances

Protein science, 2014-06, Vol.23 (6), p.747-759

2014

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Jusanin, a New Flavonoid from Artemisia commutata with an In Silico Inhibitory Potential against the SARS-CoV-2 Main Protease

Molecules (Basel, Switzerland), 2022-03, Vol.27 (5), p.1636

2022

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Exploring the Binding Effects of Natural Products and Antihypertensive Drugs on SARS-CoV-2: An In Silico Investigation of Main Protease and Spike Protein

International journal of molecular sciences, 2023-11, Vol.24 (21), p.15894

2023

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Cosolvent effects on protein stability

Annual review of physical chemistry, 2013-01, Vol.64 (1), p.273-293

2013

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A non-equilibrium approach to allosteric communication

Philosophical transactions of the Royal Society of London. Series B. Biological sciences, 2018-06, Vol.373 (1749), p.20170187

2018

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Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

Proteins, structure, function, and bioinformatics, 2014-02, Vol.82 (2), p.195-215

2014

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The Inhibition Effect of Epigallocatechin-3-Gallate on the Co-Aggregation of Amyloid-β and Human Islet Amyloid Polypeptide Revealed by Replica Exchange Molecular Dynamics Simulations

International journal of molecular sciences, 2024-02, Vol.25 (3), p.1636

2024

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Exploring the interaction of a potent anti‐cancer drug Selumetinib with bovine serum albumin: Spectral and computational attributes

Journal of molecular recognition, 2024-07, Vol.37 (4), p.e3084-n/a

2024

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Pyroglutamylation modulates electronic properties and the conformational ensemble of the amyloid β‐peptide

Proteins, structure, function, and bioinformatics, 2024-07, Vol.92 (7), p.842-853

2024

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Hydration and Structural Adaptations of the Human CYP1A1, CYP1A2, and CYP1B1 Active Sites by Molecular Dynamics Simulations

International journal of molecular sciences, 2023-07, Vol.24 (14), p.11481

2023

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Disordered linkers in multidomain allosteric proteins: Entropic effect to favor the open state or enhanced local concentration to favor the closed state?

Molecular‐dynamics simulation methods for macromolecular crystallography

Molecular Modeling in Drug Design

Identification of a conserved 8 aa insert in the PIP5K protein in the Saccharomycetaceae family of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role

Exploring ligand dynamics in protein crystal structures with ensemble refinement

Coarse-grained molecular dynamics simulations of protein-ligand binding

The putative role of some conserved water molecules in the structure and function of human transthyretin

Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods

Atomic-level characterization of protein–protein association

In silico structural characterization of Cytochrome c oxidase Subunit 1: A transmembrane protein from Aedes aegypti

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

Phytochemicals-based targeting RdRp and main protease of SARS-CoV-2 using docking and steered molecular dynamic simulation: A promising therapeutic approach for Tackling COVID-19

How does binding of agonist ligands control intrinsic molecular dynamics in human NMDA receptors?

Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field

Structural and Evolutionary Analysis Indicate That the SARS-CoV-2 Mpro Is a Challenging Target for Small-Molecule Inhibitor Design

Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine–lysine distances

Jusanin, a New Flavonoid from Artemisia commutata with an In Silico Inhibitory Potential against the SARS-CoV-2 Main Protease

Exploring the Binding Effects of Natural Products and Antihypertensive Drugs on SARS-CoV-2: An In Silico Investigation of Main Protease and Spike Protein

Cosolvent effects on protein stability

A non-equilibrium approach to allosteric communication

Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

The Inhibition Effect of Epigallocatechin-3-Gallate on the Co-Aggregation of Amyloid-β and Human Islet Amyloid Polypeptide Revealed by Replica Exchange Molecular Dynamics Simulations

Exploring the interaction of a potent anti‐cancer drug Selumetinib with bovine serum albumin: Spectral and computational attributes

Pyroglutamylation modulates electronic properties and the conformational ensemble of the amyloid β‐peptide

Hydration and Structural Adaptations of the Human CYP1A1, CYP1A2, and CYP1B1 Active Sites by Molecular Dynamics Simulations

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