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Journal articles on the topic 'MARTINI ElNeDyn force field'

Author: Grafiati

Published: 4 June 2021

Last updated: 16 February 2022

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1

López, César A., Zofie Sovova, Floris J. van Eerden, Alex H. de Vries, and Siewert J. Marrink. "Martini Force Field Parameters for Glycolipids." Journal of Chemical Theory and Computation 9, no. 3 (2013): 1694–708. http://dx.doi.org/10.1021/ct3009655.

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2

Beu, Titus Adrian, Andrada‐Elena Ailenei, and Răzvan‐Ioan Costinaş. "Martini Force Field for Protonated Polyethyleneimine." Journal of Computational Chemistry 41, no. 4 (2019): 349–61. http://dx.doi.org/10.1002/jcc.26110.

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3

Lopez, Cesar A. "Martini Force Field: Extension To Carbohydrates." Biophysical Journal 96, no. 3 (2009): 405a. http://dx.doi.org/10.1016/j.bpj.2008.12.2062.

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4

Uusitalo, Jaakko J., Helgi I. Ingólfsson, Siewert J. Marrink, and Ignacio Faustino. "Martini Coarse-Grained Force Field for RNA." Biophysical Journal 114, no. 3 (2018): 437a. http://dx.doi.org/10.1016/j.bpj.2017.11.2416.

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5

Uusitalo, Jaakko J., Helgi I. Ingólfsson, Parisa Akhshi, D. Peter Tieleman, and Siewert J. Marrink. "Martini Coarse-Grained Force Field: Extension to DNA." Journal of Chemical Theory and Computation 11, no. 8 (2015): 3932–45. http://dx.doi.org/10.1021/acs.jctc.5b00286.

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6

López, Cesar A., Andrzej J. Rzepiela, Alex H. de Vries, Lubbert Dijkhuizen, Philippe H. Hünenberger, and Siewert J. Marrink. "Martini Coarse-Grained Force Field: Extension to Carbohydrates." Journal of Chemical Theory and Computation 5, no. 12 (2009): 3195–210. http://dx.doi.org/10.1021/ct900313w.

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7

Mahajan, Subhamoy, and Tian Tang. "Comment on “Martini force field for protonated polyethyleneimine”." Journal of Computational Chemistry 42, no. 4 (2020): 261–63. http://dx.doi.org/10.1002/jcc.26453.

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8

Uusitalo, Jaakko J., Helgi I. Ingólfsson, Siewert J. Marrink, and Ignacio Faustino. "Martini Coarse-Grained Force Field: Extension to RNA." Biophysical Journal 113, no. 2 (2017): 246–56. http://dx.doi.org/10.1016/j.bpj.2017.05.043.

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9

Qi, Yifei, Helgi I. Ingólfsson, Xi Cheng, Jumin Lee, Siewert J. Marrink, and Wonpil Im. "CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field." Journal of Chemical Theory and Computation 11, no. 9 (2015): 4486–94. http://dx.doi.org/10.1021/acs.jctc.5b00513.

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10

Monticelli, Luca, Senthil K. Kandasamy, Xavier Periole, Ronald G. Larson, D. Peter Tieleman, and Siewert-Jan Marrink. "The MARTINI Coarse-Grained Force Field: Extension to Proteins." Journal of Chemical Theory and Computation 4, no. 5 (2008): 819–34. http://dx.doi.org/10.1021/ct700324x.

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11

de Jong, Djurre H., Gurpreet Singh, W. F. Drew Bennett, et al. "Improved Parameters for the Martini Coarse-Grained Protein Force Field." Journal of Chemical Theory and Computation 9, no. 1 (2012): 687–97. http://dx.doi.org/10.1021/ct300646g.

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12

Shivgan, Aishwary T., Jan K. Marzinek, Roland G. Huber, et al. "Extending the Martini Coarse-Grained Force Field to N-Glycans." Journal of Chemical Information and Modeling 60, no. 8 (2020): 3864–83. http://dx.doi.org/10.1021/acs.jcim.0c00495.

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13

Marrink, Siewert J., H. Jelger Risselada, Serge Yefimov, D. Peter Tieleman, and Alex H. de Vries. "The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations." Journal of Physical Chemistry B 111, no. 27 (2007): 7812–24. http://dx.doi.org/10.1021/jp071097f.

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14

Yesylevskyy, Semen O., Lars V. Schäfer, Durba Sengupta, and Siewert J. Marrink. "Polarizable Water Model for the Coarse-Grained MARTINI Force Field." PLoS Computational Biology 6, no. 6 (2010): e1000810. http://dx.doi.org/10.1371/journal.pcbi.1000810.

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15

Davis, Ryan S., and Mohamed Laradji. "Investigation of the Martini Force Field for Lipid Raft Membranes." Biophysical Journal 102, no. 3 (2012): 295a. http://dx.doi.org/10.1016/j.bpj.2011.11.1632.

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16

Khan, Hanif M., Paulo C. T. Souza, Sebastian Thallmair та ін. "Capturing Choline–Aromatics Cation−π Interactions in the MARTINI Force Field". Journal of Chemical Theory and Computation 16, № 4 (2020): 2550–60. http://dx.doi.org/10.1021/acs.jctc.9b01194.

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17

Negami, Tatsuki, Kentaro Shimizu, and Tohru Terada. "Protein-Ligand Binding Simulation with the Martini Coarse-Grained Force Field." Biophysical Journal 106, no. 2 (2014): 609a. http://dx.doi.org/10.1016/j.bpj.2013.11.3370.

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18

Schmalhorst, Philipp S., Felix Deluweit, Roger Scherrers, Carl-Philipp Heisenberg, and Mateusz Sikora. "Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides." Journal of Chemical Theory and Computation 13, no. 10 (2017): 5039–53. http://dx.doi.org/10.1021/acs.jctc.7b00374.

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19

Gautieri, Alfonso, Antonio Russo, Simone Vesentini, Alberto Redaelli, and Markus J. Buehler. "Coarse-Grained Model of Collagen Molecules Using an Extended MARTINI Force Field." Journal of Chemical Theory and Computation 6, no. 4 (2010): 1210–18. http://dx.doi.org/10.1021/ct100015v.

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20

Periole, Xavier, Siewert-Jan Marrink, and Peter Tieleman. "A Structurally Flexible Protein Backbone for the MARTINI Coarse Grained Force Field." Biophysical Journal 100, no. 3 (2011): 613a. http://dx.doi.org/10.1016/j.bpj.2010.12.3533.

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21

Uusitalo, Jaakko J., Helgi I. Ingólfsson, and Siewert-Jan Marrink. "Covering All the Bases: A Martini Coarse-Grained Force Field for DNA." Biophysical Journal 104, no. 2 (2013): 169a. http://dx.doi.org/10.1016/j.bpj.2012.11.952.

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22

Uusitalo, Jaakko, Helgi I. Ingólfsson, Parisa Akhshi, et al. "Coarse-Grained Modeling of DNA-Vesicle Systems with the Martini Force Field." Biophysical Journal 106, no. 2 (2014): 803a. http://dx.doi.org/10.1016/j.bpj.2013.11.4402.

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23

Stachiewicz, Anna, and Andrzej Molski. "A coarse-grained MARTINI-like force field for DNA unzipping in nanopores." Journal of Computational Chemistry 36, no. 13 (2015): 947–56. http://dx.doi.org/10.1002/jcc.23874.

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24

Souza, Paulo C. T., Riccardo Alessandri, Jonathan Barnoud, et al. "Martini 3: a general purpose force field for coarse-grained molecular dynamics." Nature Methods 18, no. 4 (2021): 382–88. http://dx.doi.org/10.1038/s41592-021-01098-3.

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25

Marchetto, Alessandro, Zeineb Si Chaib, Carlo Alberto Rossi, et al. "CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations." Molecules 25, no. 24 (2020): 5934. http://dx.doi.org/10.3390/molecules25245934.

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Advances in coarse-grained molecular dynamics (CGMD) simulations have extended the use of computational studies on biological macromolecules and their complexes, as well as the interactions of membrane protein and lipid complexes at a reduced level of representation, allowing longer and larger molecular dynamics simulations. Here, we present a computational platform dedicated to the preparation, running, and analysis of CGMD simulations. The platform is built on a completely revisited version of our Martini coarsE gRained MembrAne proteIn Dynamics (MERMAID) web server, and it integrates this w

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26

Vazquez-Salazar, Luis Itza, Michele Selle, Alex H. de Vries, Siewert J. Marrink, and Paulo C. T. Souza. "Martini coarse-grained models of imidazolium-based ionic liquids: from nanostructural organization to liquid–liquid extraction." Green Chemistry 22, no. 21 (2020): 7376–86. http://dx.doi.org/10.1039/d0gc01823f.

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New coarse-grained models for imidazolium-based ionic liquids (ILs) were developed using the Martini force field. They were able to not only reproduce the structural properties but also allow simulations of liquid–liquid extraction experiments.

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27

Banerjee, Pallavi, Sudip Roy, and Nitish Nair. "Coarse-Grained Molecular Dynamics Force-Field for Polyacrylamide in Infinite Dilution Derived from Iterative Boltzmann Inversion and MARTINI Force-Field." Journal of Physical Chemistry B 122, no. 4 (2018): 1516–24. http://dx.doi.org/10.1021/acs.jpcb.7b09019.

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28

Fegan, Sarah K., and Mark Thachuk. "Suitability of the MARTINI Force Field for Use with Gas-Phase Protein Complexes." Journal of Chemical Theory and Computation 8, no. 4 (2012): 1304–13. http://dx.doi.org/10.1021/ct200739s.

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29

Rossi, Giulia, Luca Monticelli, Sakari R. Puisto, Ilpo Vattulainen, and Tapio Ala-Nissila. "Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case." Soft Matter 7, no. 2 (2011): 698–708. http://dx.doi.org/10.1039/c0sm00481b.

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30

Bereau, Tristan, and Kurt Kremer. "Automated Parametrization of the Coarse-Grained Martini Force Field for Small Organic Molecules." Journal of Chemical Theory and Computation 11, no. 6 (2015): 2783–91. http://dx.doi.org/10.1021/acs.jctc.5b00056.

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31

Zhang, Xiaohua, Shiv Sundram, Tomas Oppelstrup, et al. "ddcMD: A fully GPU-accelerated molecular dynamics program for the Martini force field." Journal of Chemical Physics 153, no. 4 (2020): 045103. http://dx.doi.org/10.1063/5.0014500.

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32

Risselada, H. Jelger. "Martini 3: a coarse-grained force field with an eye for atomic detail." Nature Methods 18, no. 4 (2021): 342–43. http://dx.doi.org/10.1038/s41592-021-01111-9.

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33

Arnarez, Clément, Jaakko J. Uusitalo, Marcelo F. Masman, et al. "Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simulations with Implicit Solvent." Journal of Chemical Theory and Computation 11, no. 1 (2014): 260–75. http://dx.doi.org/10.1021/ct500477k.

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34

Davis, Ryan S., P. B. Sunil Kumar, Maria Maddalena Sperotto, and Mohamed Laradji. "Predictions of Phase Separation in Three-Component Lipid Membranes by the MARTINI Force Field." Journal of Physical Chemistry B 117, no. 15 (2013): 4072–80. http://dx.doi.org/10.1021/jp4000686.

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35

Miguel, Virginia, Maria A. Perillo, and Marcos A. Villarreal. "Improved prediction of bilayer and monolayer properties using a refined BMW-MARTINI force field." Biochimica et Biophysica Acta (BBA) - Biomembranes 1858, no. 11 (2016): 2903–10. http://dx.doi.org/10.1016/j.bbamem.2016.08.016.

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36

Carpenter, Timothy S., Cesar A. López, Chris Neale, et al. "Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field." Journal of Chemical Theory and Computation 14, no. 11 (2018): 6050–62. http://dx.doi.org/10.1021/acs.jctc.8b00496.

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37

Atsmon-Raz, Yoav, and D. Peter Tieleman. "Parameterization of Palmitoylated Cysteine, Farnesylated Cysteine, Geranylgeranylated Cysteine, and Myristoylated Glycine for the Martini Force Field." Journal of Physical Chemistry B 121, no. 49 (2017): 11132–43. http://dx.doi.org/10.1021/acs.jpcb.7b10175.

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38

Zhang, Lin, Shu Bai, and Yan Sun. "Modification of Martini force field for molecular dynamics simulation of hydrophobic charge induction chromatography of lysozyme." Journal of Molecular Graphics and Modelling 29, no. 7 (2011): 906–14. http://dx.doi.org/10.1016/j.jmgm.2011.02.004.

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39

Potter, Thomas D., Elin L. Barrett, and Mark A. Miller. "Automated Coarse-Grained Mapping Algorithm for the Martini Force Field and Benchmarks for Membrane–Water Partitioning." Journal of Chemical Theory and Computation 17, no. 9 (2021): 5777–91. http://dx.doi.org/10.1021/acs.jctc.1c00322.

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40

Ndao, Makha, Julien Devémy, Aziz Ghoufi, and Patrice Malfreyt. "Coarse-Graining the Liquid–Liquid Interfaces with the MARTINI Force Field: How Is the Interfacial Tension Reproduced?" Journal of Chemical Theory and Computation 11, no. 8 (2015): 3818–28. http://dx.doi.org/10.1021/acs.jctc.5b00149.

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41

Michalowsky, Julian, Lars V. Schäfer, Christian Holm, and Jens Smiatek. "A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions." Journal of Chemical Physics 146, no. 5 (2017): 054501. http://dx.doi.org/10.1063/1.4974833.

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42

Li, Hualin, and Alemayehu A. Gorfe. "Aggregation of Lipid-Anchored Full-Length H-Ras in Lipid Bilayers: Simulations with the MARTINI Force Field." PLoS ONE 8, no. 7 (2013): e71018. http://dx.doi.org/10.1371/journal.pone.0071018.

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43

Lamprakis, Christos, Ioannis Andreadelis, John Manchester, Camilo Velez-Vega, José S. Duca, and Zoe Cournia. "Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments." Journal of Chemical Theory and Computation 17, no. 5 (2021): 3088–102. http://dx.doi.org/10.1021/acs.jctc.0c00507.

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44

Chakraborty, Srirupa, Kshitij Wagh, S. Gnanakaran, and Cesar A. López. "Development of Martini 2.2 parameters for N-glycans: a case study of the HIV-1 Env glycoprotein dynamics." Glycobiology 31, no. 7 (2021): 787–99. http://dx.doi.org/10.1093/glycob/cwab017.

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Abstract N-linked glycans are ubiquitous in nature and play key roles in biology. For example, glycosylation of pathogenic proteins is a common immune evasive mechanism, hampering the development of successful vaccines. Due to their chemical variability and complex dynamics, an accurate molecular understanding of glycans is still limited by the lack of effective resolution of current experimental approaches. Here, we have developed and implemented a reductive model based on the popular Martini 2.2 coarse-grained force field for the computational study of N-glycosylation. We used the HIV-1 Env

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45

Negami, Tatsuki, Tohru Terada, and Kentaro Shimizu. "2P044 Comparative simulations of protein-ligand binding processes using the MARTINI coarse-grained force field(01B. Protein: Structure & Function,Poster)." Seibutsu Butsuri 53, supplement1-2 (2013): S166. http://dx.doi.org/10.2142/biophys.53.s166_2.

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46

Nawaz, Selina, and Paola Carbone. "Coarse-Graining Poly(ethylene oxide)–Poly(propylene oxide)–Poly(ethylene oxide) (PEO–PPO–PEO) Block Copolymers Using the MARTINI Force Field." Journal of Physical Chemistry B 118, no. 6 (2014): 1648–59. http://dx.doi.org/10.1021/jp4092249.

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47

Maftouni, N., M. Amininassab, M. N. Mello, and S. Marink. "Nanocomputation of Mechanical Properties in Nanobio Membrane." Applied Mechanics and Materials 110-116 (October 2011): 3883–87. http://dx.doi.org/10.4028/www.scientific.net/amm.110-116.3883.

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It is very essential to know mechanical properties in different regions of nanobio membrane as one of the most important parts of living systems. Here the coarse-grained (CG) simulations method have been used to study the pressure profile in a system including nanobio membrane and water. CG simulations have become an important tool to study many biomolecular processes, exploring scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals p

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48

Stark, Austin C., Casey T. Andrews, and Adrian H. Elcock. "Toward Optimized Potential Functions for Protein–Protein Interactions in Aqueous Solutions: Osmotic Second Virial Coefficient Calculations Using the MARTINI Coarse-Grained Force Field." Journal of Chemical Theory and Computation 9, no. 9 (2013): 4176–85. http://dx.doi.org/10.1021/ct400008p.

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49

Nawaz, Selina, and Paola Carbone. "Correction to “Coarse-Graining Poly(ethylene-oxide)–Poly(propylene-oxide)–Poly(ethylene-oxide) (PEO–PPO–PEO) Block Copolymers Using the MARTINI Force Field”." Journal of Physical Chemistry B 119, no. 7 (2015): 3332. http://dx.doi.org/10.1021/acs.jpcb.5b00565.

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50

Zalewski, Mateusz, Sebastian Kmiecik, and Michał Koliński. "Molecular Dynamics Scoring of Protein–Peptide Models Derived from Coarse-Grained Docking." Molecules 26, no. 11 (2021): 3293. http://dx.doi.org/10.3390/molecules26113293.

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One of the major challenges in the computational prediction of protein–peptide complexes is the scoring of predicted models. Usually, it is very difficult to find the most accurate solutions out of the vast number of sometimes very different and potentially plausible predictions. In this work, we tested the protocol for Molecular Dynamics (MD)-based scoring of protein–peptide complex models obtained from coarse-grained (CG) docking simulations. In the first step of the scoring procedure, all models generated by CABS-dock were reconstructed starting from their original C-alpha trace representat

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