atomistic molecular dynamics simulations (Molecular Dynamics Inc)

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Molecular Dynamics Inc atomistic molecular dynamics simulations
Atomistic Molecular Dynamics Simulations, supplied by Molecular Dynamics Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/atomistic+molecular+dynamics/atomistic+dynamics+molecular+simulations/pm42275451-402-7-8
Average 86 stars, based on 1 article reviews

atomistic molecular dynamics simulations - by Bioz Stars, 2026-11

86/100 stars

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Article Title: Intramolecular bonding as a design strategy for robust intermolecular binding of oligomers.
Article Snippet: Atomistic Molecular Dynamics (MD).

Article Title: Comparative Evaluation of Explicit Solvent Models for RNA-Ligand Docking.
Article Snippet: On the Power and Challenges of Atomistic Molecular Dynamics to Investigate RNA Molecules.

Article Title: Structural organization of HBV pgRNA genome driven by phase separation in capsid confinement
Article Snippet: At λ = 0.7, the coarse-grained model accurately reproduced the average root mean square fluctuation (RMSF) of HBV capsid protein dimers obtained from previous atomistic molecular dynamics (MD) simulations. . For the nucleotide acids, the three-site-per-nucleotide model (3SPN.2) was adopted.

Article Title: Critical Assessment of a Structure-Based Pipeline for Targeting the Long Noncoding RNA MALAT1.
Article Snippet: 2014, 112, 379−384. (62) Muscat, S.; Martino, G.; Manigrasso, J.; Marcia, M.; De Vivo, M. On the Power and Challenges of Atomistic Molecular Dynamics to Investigate RNA Molecules.

Cryo-EM Sample Prep:

Article Title: Role of Small Membrane Proteins in the Green Sulfur Bacterial Reaction Center
Article Snippet: .. This study addresses this gap by applying cutting-edge computational approaches, specifically atomistic molecular dynamics (MD) combined with graph network analysis, ensuring consistency with cryogenic electron microscopy (Cryo-EM) electron densities, to dissect the regulatory mechanism of the Green Sulfur Bacterial Photosynthetic Reaction Center (GSB-RC). ..

Sequencing:

Article Title: From biomolecular condensates to functional nanomaterials: LLPS-inspired frameworks for nanoscale hydrogels and adaptive materials
Article Snippet: .. Current computational approaches often work within a single scale, such as atomistic molecular dynamics [ ], mesoscale viscoelastic models [ ], or continuum thermodynamics [ ], and thus fail to capture the full cascade from sequence-level interactions to emergent condensate mechanics under nanoparticle influence. ..

Sampling:

Article Title: Free Energy Calculation Method Based on Enhanced Sampling of Diverse Protein Conformations Predicted by Artificial Intelligence.
Article Snippet: .. Exploring Large Domain Motions in Proteins Using Atomistic Molecular Dynamics with Enhanced Conformational Sampling. ..

Binding Assay:

Article Title: Correction: Mechanism of RGD-conjugated nanodevice binding to its target protein integrin α V β 3 by atomistic molecular dynamics and machine learning.
Article Snippet: .. CORRECTION Cite this: DOI: 10.1039/d6nr90037b DOI: 10.1039/d6nr90037b rsc.li/nanoscale Correction: Mechanism of RGD-conjugated nanodevice binding to its target protein integrin αVβ3 by atomistic molecular dynamics and machine learning Giulia Frigerio,a Edoardo Donadoni,a Paulo Siani,a Jacopo Vertemara,b Stefano Motta,c Laura Bonati,c Luca De Gioiab and Cristiana Di Valentin*a,d Correction for ‘Mechanism of RGD-conjugated nanodevice binding to its target protein integrin αVβ3 by atomistic molecular dynamics and machine learning’ by Giulia Frigerio et al., Nanoscale, 2024, 16, 4063–4081, https://doi.org/10.1039/D3NR05123D. ..

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