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Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods

2010

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Multiscale computational simulation of pollutant behavior at water interfaces

Water research (Oxford), 2024-02, Vol.250, p.121043-121043, Article 121043

2024

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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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Anisotropic Friction in a Ligand-Protein Complex

Nano letters, 2023-05, Vol.23 (10), p.4111-4119

2023

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Molecular Binding Mechanism and Pharmacology Comparative Analysis of Noscapine for Repurposing against SARS-CoV‑2 Protease

Journal of proteome research, 2020-11, Vol.19 (11), p.4678-4689

2020

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Binding of Capsaicin to the TRPV1 Ion Channel

Molecular pharmaceutics, 2015-12, Vol.12 (12), p.4454-4465

2015

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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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The penetration of human defensin 5 (HD5) through bacterial outer membrane: simulation studies

Journal of molecular modeling, 2021-10, Vol.27 (10), p.291-291, Article 291

2021

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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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Insights from molecular dynamics simulations and steered molecular dynamics simulations to exploit new trends of the interaction between HIF-1α and p300

Journal of biomolecular structure & dynamics, 2020-01, Vol.38 (1), p.1-12

2020

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Binding hotspots on K-ras: Consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis

Proteins, structure, function, and bioinformatics, 2015-05, Vol.83 (5), p.898-909

2015

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Imidazole[1,5-a]pyridine derivatives as EGFR tyrosine kinase inhibitors unraveled by umbrella sampling and steered molecular dynamics simulations

Scientific reports, 2024-05, Vol.14 (1), p.12218-12218, Article 12218

2024

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Molecular docking, validation, dynamics simulations, and pharmacokinetic prediction of natural compounds against the SARS-CoV-2 main-protease

Journal of biomolecular structure & dynamics, 2022-02, Vol.40 (2), p.585-611

2022

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Integration of Molecular Docking Analysis and Molecular Dynamics Simulations for Studying Food Proteins and Bioactive Peptides

Journal of agricultural and food chemistry, 2022-02, Vol.70 (4), p.934-943

2022

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Real-World Predictions from Ab Initio Molecular Dynamics Simulations

Multiscale Molecular Methods in Applied Chemistry, 2012, Vol.307, p.109-153

2012

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Complete reconstruction of dasatinib unbinding pathway from c-Src kinase by supervised molecular dynamics simulation method; assessing efficiency and trustworthiness of the method

Journal of biomolecular structure & dynamics, 2022-01, Vol.40 (23), p.12535-12545

2022

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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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Rationally designed peptide nanosponges for cell-based cancer therapy

Nanomedicine, 2017-11, Vol.13 (8), p.2555-2564

2017

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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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How cholesterol stiffens unsaturated lipid membranes

Proceedings of the National Academy of Sciences - PNAS, 2020-09, Vol.117 (36), p.21896-21905

2020

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MD simulations reveal alternate conformations of the oxyanion hole in the Zika virus NS2B/NS3 protease

Proteins, structure, function, and bioinformatics, 2020-02, Vol.88 (2), p.345-354

2020

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Liquid Structure with Nano-Heterogeneity Promotes Cationic Transport in Concentrated Electrolytes

ACS nano, 2017-10, Vol.11 (10), p.10462-10471

2017

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Structural insights into the synthesis of FMN in prokaryotic organisms

Acta crystallographica. Section D, Biological crystallography., 2015-12, Vol.71 (12), p.2526-2542

2015

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Computational simulation and statistical analysis on the relationship between corrosion inhibition efficiency and molecular structure of some hydrazine derivatives in phosphoric acid on mild steel surface

Applied surface science, 2019-10, Vol.491, p.707-722

2019

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Advances in Computer Simulation Studies on Crystal Growth

Nada, Hiroki

2018

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