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The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.
Rizzi A, Jensen T, Slochower DR, Aldeghi M, Gapsys V, Ntekoumes D, Bosisio S, Papadourakis M, Henriksen NM, de Groot BL, Cournia Z, Dickson A, Michel J, Gilson MK, Shirts MR, Mobley DL, Chodera JD. Rizzi A, et al. Among authors: de groot bl. J Comput Aided Mol Des. 2020 May;34(5):601-633. doi: 10.1007/s10822-020-00290-5. Epub 2020 Jan 27. J Comput Aided Mol Des. 2020. PMID: 31984465 Free PMC article.
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
208 results