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Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods

Marx, Dominik

2009

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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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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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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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Unlocking bacterial defense: Exploring the potent inhibition of NorA efflux pump by coumarin derivatives in Staphylococcus aureus

Microbial pathogenesis, 2024-05, Vol.190, p.106608-106608, Article 106608

2024

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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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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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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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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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Advances in Computer Simulation Studies on Crystal Growth

Nada, Hiroki

2018

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Molecular Modeling in Drug Design

2019

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A conformational landscape for alginate secretion across the outer membrane of Pseudomonas aeruginosa

Acta crystallographica. Section D, Biological crystallography., 2014-08, Vol.70 (8), p.2054-2068

2014

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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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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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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 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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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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Capture of H2S from binary gas mixture by imidazolium-based ionic liquids with nonfluorous anions: A theoretical study

AIChE journal, 2013-10, Vol.59 (10), p.3824-3833

2013

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

Fuxreiter, Monika

1, 2014

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How do carbon nanotubes serve as carriers for gemcitabine transport in a drug delivery system?

Journal of molecular graphics & modelling, 2011-02, Vol.29 (5), p.591-596

2011

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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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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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