D
Djurre H. de Jong
Researcher at University of Groningen
Publications - 23
Citations - 3397
Djurre H. de Jong is an academic researcher from University of Groningen. The author has contributed to research in topics: Membrane & Lipid bilayer. The author has an hindex of 18, co-authored 23 publications receiving 2770 citations. Previous affiliations of Djurre H. de Jong include University of Münster.
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Journal ArticleDOI
Improved Parameters for the Martini Coarse-Grained Protein Force Field
Djurre H. de Jong,Gurpreet Singh,W. F. Drew Bennett,Clement Arnarez,Tsjerk A. Wassenaar,Lars V. Schäfer,Xavier Periole,D. Peter Tieleman,Siewert J. Marrink +8 more
TL;DR: Improve some of the bonded terms in the Martini protein force field that lead to a more realistic length of α-helices and to improved numerical stability for polyalanine and glycine repeats.
Journal ArticleDOI
The power of coarse graining in biomolecular simulations
Helgi I. Ingólfsson,Cesar A. Lopez,Jaakko J. Uusitalo,Djurre H. de Jong,Srinivasa M. Gopal,Xavier Periole,Siewert J. Marrink +6 more
TL;DR: An overview of some of the more popular CG models used in biomolecular applications to date, focusing on models that retain chemical specificity, are provided.
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Martini straight: Boosting performance using a shorter cutoff and GPUs
TL;DR: It is concluded that the newly proposed straight cutoff approach is a viable alternative to the standard shifted potentials used in Martini, offering significant speedup even in the absence of GPUs.
Journal ArticleDOI
Dry Martini, a coarse-grained force field for lipid membrane simulations with implicit solvent.
Clement Arnarez,Jaakko J. Uusitalo,Marcelo F. Masman,Helgi I. Ingólfsson,Djurre H. de Jong,Manuel N. Melo,Xavier Periole,Alex H. de Vries,Siewert J. Marrink +8 more
TL;DR: An implicit-solvent version of the popular CG Martini model, nicknamed "Dry" Martini, is introduced, to account for the omitted solvent degrees of freedom, and the nonbonded interaction matrix underlying the Martini force field was reparametrized.
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Phytochemicals Perturb Membranes and Promiscuously Alter Protein Function
Helgi I. Ingólfsson,Pratima Thakur,Karl F. Herold,E. Ashley Hobart,Nicole Ramsey,Xavier Periole,Djurre H. de Jong,Martijn Zwama,Duygu Yilmaz,Katherine C. Hall,Thorsten Maretzky,Hugh C. Hemmings,Carl P. Blobel,Siewert J. Marrink,Armagan Kocer,Jon T. Sack,Olaf S. Andersen +16 more
TL;DR: The results suggest that many effects of amphiphilic phytochemicals are due to cell membrane perturbations, rather than specific protein binding, which is consistent with a common, bilayer-mediated mechanism.