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Page 1
Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.
Wieczór M, Genna V, Aranda J, Badia RM, Gelpí JL, Gapsys V, de Groot BL, Lindahl E, Municoy M, Hospital A, Orozco M. Wieczór M, et al. Among authors: de groot bl. Wiley Interdiscip Rev Comput Mol Sci. 2022 May 30:e1622. doi: 10.1002/wcms.1622. Online ahead of print. Wiley Interdiscip Rev Comput Mol Sci. 2022. PMID: 35935573 Free PMC article.
Speeding up parallel GROMACS on high-latency networks.
Kutzner C, van der Spoel D, Fechner M, Lindahl E, Schmitt UW, de Groot BL, Grubmüller H. Kutzner C, et al. Among authors: de groot bl. J Comput Chem. 2007 Sep;28(12):2075-84. doi: 10.1002/jcc.20703. J Comput Chem. 2007. PMID: 17405124
Optimal superpositioning of flexible molecule ensembles.
Gapsys V, de Groot BL. Gapsys V, et al. Among authors: de groot bl. Biophys J. 2013 Jan 8;104(1):196-207. doi: 10.1016/j.bpj.2012.11.003. Epub 2013 Jan 8. Biophys J. 2013. PMID: 23332072 Free PMC article.
Computational analysis of local membrane properties.
Gapsys V, de Groot BL, Briones R. Gapsys V, et al. Among authors: de groot bl. J Comput Aided Mol Des. 2013 Oct;27(10):845-58. doi: 10.1007/s10822-013-9684-0. Epub 2013 Oct 23. J Comput Aided Mol Des. 2013. PMID: 24150904 Free PMC article.
Phosphorylation drives a dynamic switch in serine/arginine-rich proteins.
Xiang S, Gapsys V, Kim HY, Bessonov S, Hsiao HH, Möhlmann S, Klaukien V, Ficner R, Becker S, Urlaub H, Lührmann R, de Groot B, Zweckstetter M. Xiang S, et al. Structure. 2013 Dec 3;21(12):2162-74. doi: 10.1016/j.str.2013.09.014. Epub 2013 Oct 31. Structure. 2013. PMID: 24183573 Free article.
Calculation of binding free energies.
Gapsys V, Michielssens S, Peters JH, de Groot BL, Leonov H. Gapsys V, et al. Among authors: de groot bl. Methods Mol Biol. 2015;1215:173-209. doi: 10.1007/978-1-4939-1465-4_9. Methods Mol Biol. 2015. PMID: 25330964
214 results