Martini 3
| Autor: | Vincent Nieto, Valentina Corradi, Siewert J. Marrink, Matti Javanainen, Peter C. Kroon, Ilpo Vattulainen, Hector Martinez-Seara, D. Peter Tieleman, Alex H. de Vries, Jan Domański, Hanif M. Khan, Robert B. Best, Ilias Patmanidis, Sebastian Thallmair, Ignacio Faustino, Xavier Periole, Jonathan Barnoud, Tsjerk A. Wassenaar, Josef Melcr, Nathalie Reuter, Haleh Abdizadeh, Bart M H Bruininks, Paulo C. T. Souza, Fabian Grünewald, Riccardo Alessandri, Luca Monticelli |
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| Přispěvatelé: | Department of Physics, Molecular Dynamics |
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
STRUCTURAL BASIS
Materials science Lipid Bilayers TRANSITIONS Molecular Dynamics Simulation SOLUBILITY Molecular systems Biochemistry Miscibility Force field (chemistry) PROTEIN-PROTEIN INTERACTIONS 03 medical and health sciences Molecular dynamics Polarizability Molecular Biology 030304 developmental biology 0303 health sciences Computational model Hydrogen Bonding ASSOCIATION Cell Biology TRANSMEMBRANE DOMAIN SIMULATIONS TRANSMEMBRANE DOMAIN DIMERIZATION MODEL General purpose Chemical physics Thermodynamics 1182 Biochemistry cell and molecular biology Computational biophysics HELIX INTERACTIONS EXTENSION Biotechnology |
| Zdroj: | Nature Methods, 18, 382-388. Nature Publishing Group Nature Methods Souza, P C T, Alessandri, R, Barnoud, J, Thallmair, S, Faustino, I, Grünewald, F, Patmanidis, I, Abdizadeh, H, Bruininks, B M H, Wassenaar, T A, Kroon, P C, Melcr, J, Nieto, V, Corradi, V, Khan, H M, Domański, J, Javanainen, M, Martinez-Seara, H, Reuter, N, Best, R B, Vattulainen, I, Monticelli, L, Periole, X, Tieleman, D P, de Vries, A H & Marrink, S J 2021, ' Martini 3 : a general purpose force field for coarse-grained molecular dynamics ', Nature Methods, vol. 18, no. 4, pp. 382-388 . https://doi.org/10.1038/s41592-021-01098-3 |
| ISSN: | 1548-7105 |
| DOI: | 10.1038/s41592-021-01098-3 |
| Popis: | The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 (http://cgmartini.nl), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability. The updated model allows more accurate predictions of molecular packing and interactions in general, which is exemplified with a vast and diverse set of applications, ranging from oil/water partitioning and miscibility data to complex molecular systems, involving protein-protein and protein-lipid interactions and material science applications as ionic liquids and aedamers. |
| Databáze: | OpenAIRE |
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