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Page 1
Towards design of drugs and delivery systems with the Martini coarse-grained model.
Kjølbye LR, Pereira GP, Bartocci A, Pannuzzo M, Albani S, Marchetto A, Jiménez-García B, Martin J, Rossetti G, Cecchini M, Wu S, Monticelli L, Souza PCT. Kjølbye LR, et al. QRB Discov. 2022 Oct 12;3:e19. doi: 10.1017/qrd.2022.16. eCollection 2022. QRB Discov. 2022. PMID: 37529288 Free PMC article. Review.
Coarse-grained (CG) modelling with the Martini force field has come of age. By combining a variety of bead types and sizes with a new mapping approach, the newest version of the model is able to accurately simulate large biomolecular complexes at millisecond …
Coarse-grained (CG) modelling with the Martini force field has come of age. By combining a variety of bead types and sizes wit …
The Martini Model in Materials Science.
Alessandri R, Grünewald F, Marrink SJ. Alessandri R, et al. Adv Mater. 2021 Jun;33(24):e2008635. doi: 10.1002/adma.202008635. Epub 2021 May 6. Adv Mater. 2021. PMID: 33956373
The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Here, the main applications to date of the Martini model in materials science are highlighted, and a perspective for the future d …
The model's underlying building block principle does not pose restrictions on its application beyond biomolecular systems. Her …
Perspective on the Martini model.
Marrink SJ, Tieleman DP. Marrink SJ, et al. Chem Soc Rev. 2013 Aug 21;42(16):6801-22. doi: 10.1039/c3cs60093a. Chem Soc Rev. 2013. PMID: 23708257 Review.
The Martini model, a coarse-grained force field for biomolecular simulations, has found a broad range of applications since its release a decade ago. ...Here we review the current state of the model. We describe recent highlights as well as shortcomings, and …
The Martini model, a coarse-grained force field for biomolecular simulations, has found a broad range of applications since it …
Pitfalls of the Martini Model.
Alessandri R, Souza PCT, Thallmair S, Melo MN, de Vries AH, Marrink SJ. Alessandri R, et al. J Chem Theory Comput. 2019 Oct 8;15(10):5448-5460. doi: 10.1021/acs.jctc.9b00473. Epub 2019 Sep 24. J Chem Theory Comput. 2019. PMID: 31498621 Free PMC article.
Building block based CG models, such as the Martini model, possess the key advantage of allowing for a broad range of applications without the need to reparametrize the force field each time. ...Moreover, we show that too weak bonded force constants entail th …
Building block based CG models, such as the Martini model, possess the key advantage of allowing for a broad range of a …
Martini coarse-grained model for polyethylenimine.
Mahajan S, Tang T. Mahajan S, et al. J Comput Chem. 2019 Jan 30;40(3):607-618. doi: 10.1002/jcc.25747. Epub 2018 Nov 10. J Comput Chem. 2019. PMID: 30414204
Here we present the methodology to systematically categorize bond lengths, bond angles and dihedral angles, which allows us to model branched PEIs. The CG model was developed under the Martini scheme based on eight ~600 Da PEIs, with four different degree of …
Here we present the methodology to systematically categorize bond lengths, bond angles and dihedral angles, which allows us to model …
Optimizing Go-MARTINI Coarse-Grained Model for F-BAR Protein on Lipid Membrane.
Mahmood MI, Poma AB, Okazaki KI. Mahmood MI, et al. Front Mol Biosci. 2021 Feb 22;8:619381. doi: 10.3389/fmolb.2021.619381. eCollection 2021. Front Mol Biosci. 2021. PMID: 33693028 Free PMC article.
Using the Go-MARTINI model, we conduct MD simulations of the F-BAR Pacsin1 protein on lipid membrane. ...With the optimized Go-MARTINI model, we show that it reproduces structural fluctuations of the Pacsin1 dimer from atomistic simulations. ...
Using the Go-MARTINI model, we conduct MD simulations of the F-BAR Pacsin1 protein on lipid membrane. ...With the optimized Go …
Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides.
Moreira RA, Weber SAL, Poma AB. Moreira RA, et al. Molecules. 2022 Feb 1;27(3):976. doi: 10.3390/molecules27030976. Molecules. 2022. PMID: 35164241 Free PMC article.
High resolution data from all-atom molecular simulations is used to parameterize a Martini 3 coarse-grained (CG) model of cellulose I allomorphs and cellulose type-II fibrils. ...Furthermore, our CG model poses a very small deviation from the native-like stru …
High resolution data from all-atom molecular simulations is used to parameterize a Martini 3 coarse-grained (CG) model of cell …
Transferable MARTINI Model of Poly(ethylene Oxide).
Grunewald F, Rossi G, de Vries AH, Marrink SJ, Monticelli L. Grunewald F, et al. J Phys Chem B. 2018 Jul 26;122(29):7436-7449. doi: 10.1021/acs.jpcb.8b04760. Epub 2018 Jul 13. J Phys Chem B. 2018. PMID: 29966087
Motivated by the deficiencies of the previous MARTINI models of poly(ethylene oxide) (PEO), we present a new model featuring a high degree of transferability. ...Overall, the new PEO model outperforms previous models and features a high degree o …
Motivated by the deficiencies of the previous MARTINI models of poly(ethylene oxide) (PEO), we present a new model feat …
Martini Coarse-Grained Model of Hyaluronic Acid for the Structural Change of Its Gel in the Presence of Monovalent and Divalent Salts.
Kumar R, Lee YK, Jho YS. Kumar R, et al. Int J Mol Sci. 2020 Jun 29;21(13):4602. doi: 10.3390/ijms21134602. Int J Mol Sci. 2020. PMID: 32610441 Free PMC article.
To overcome this limitation, we developed a coarse grained (CG) model for HA adapting the Martini scheme. A very good agreement was observed between the CG model and all-atom simulations for both local (bonded interactions) and global properties (end-to-end d …
To overcome this limitation, we developed a coarse grained (CG) model for HA adapting the Martini scheme. A very good agreemen …
Martini Coarse-Grained Model for Clay-Polymer Nanocomposites.
Khan P, Goel G. Khan P, et al. J Phys Chem B. 2019 Oct 24;123(42):9011-9023. doi: 10.1021/acs.jpcb.9b06708. Epub 2019 Oct 15. J Phys Chem B. 2019. PMID: 31573809
We have developed a coarse-grained (CG) model of a polymer-clay system consisting of organically modified montmorillonite (oMMT) nanoclay as the nanoparticle in accordance with the MARTINI force field. ...Individual dispersive and polar contributions to oMMT cleavag …
We have developed a coarse-grained (CG) model of a polymer-clay system consisting of organically modified montmorillonite (oMMT) nano …
3,094 results