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Assessing the Martini 3 protein model: A review of its path and potential
Coarse-grained (CG) protein models have become indispensable tools for studying many
biological protein details, from conformational dynamics to the organization of protein macro …
biological protein details, from conformational dynamics to the organization of protein macro …
Plant protein–lipid interfaces studied by molecular dynamics simulations
M Neubergerová, R Pleskot - Journal of Experimental Botany, 2024 - academic.oup.com
The delineation of protein–lipid interfaces is essential for understanding the mechanisms of
various membrane-associated processes crucial to plant development and growth, including …
various membrane-associated processes crucial to plant development and growth, including …
GōMartini 3: from large conformational changes in proteins to environmental bias corrections
Coarse-grained modeling has become an important tool to supplement experimental
measurements, allowing access to spatio-temporal scales beyond all-atom based …
measurements, allowing access to spatio-temporal scales beyond all-atom based …
Switching Go̅-Martini for Investigating Protein Conformational Transitions and Associated Protein–Lipid Interactions
Proteins are dynamic biomolecules that can transform between different conformational
states when exerting physiological functions, which is difficult to simulate using all-atom …
states when exerting physiological functions, which is difficult to simulate using all-atom …
Martini 3 OliGo̅mers: a scalable approach for multimers and fibrils in GROMACS
K Korshunova, J Kiuru, J Liekkinen… - Journal of Chemical …, 2024 - ACS Publications
Martini 3 is a widely used coarse-grained simulation method for large-scale biomolecular
simulations. It can be combined with a Go̅ model to realistically describe higher-order …
simulations. It can be combined with a Go̅ model to realistically describe higher-order …
[HTML][HTML] ezAlign: A Tool for Converting Coarse-Grained Molecular Dynamics Structures to Atomistic Resolution for Multiscale Modeling
Soft condensed matter is challenging to study due to the vast time and length scales that are
necessary to accurately represent complex systems and capture their underlying physics …
necessary to accurately represent complex systems and capture their underlying physics …
[PDF][PDF] Building complex membranes with Martini 3
The Martini model is a popular force field for coarse-grained simulations. Membranes have
always been at the center of its development, with the latest version, Martini 3, showing great …
always been at the center of its development, with the latest version, Martini 3, showing great …
Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery
Lipid-mediated delivery of active pharmaceutical ingredients (API) opened new possibilities
in advanced therapies. By encapsulating an API into a lipid nanocarrier (LNC), one can …
in advanced therapies. By encapsulating an API into a lipid nanocarrier (LNC), one can …
Optimized Protein–Excipient Interactions in the Martini 3 Force Field
High drug dosages required for biotherapeutics, such as monoclonal antibodies (mAbs),
and the small volumes that can be administered to patients via subcutaneous injections …
and the small volumes that can be administered to patients via subcutaneous injections …
Insertion and anchoring of HIV-1 fusion peptide into complex membrane mimicking the human T cell
The N-terminus of the gp41 subunit for the HIV-1 envelope protein, also known as the fusion
peptide, consists of 15 to 22 highly conserved hydrophobic residues. The HIV-1 fusion …
peptide, consists of 15 to 22 highly conserved hydrophobic residues. The HIV-1 fusion …