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A probabilistic model of RNA conformational space.
Frellsen J, Moltke I, Thiim M, Mardia KV, Ferkinghoff-Borg J, Hamelryck T. Frellsen J, et al. Among authors: hamelryck t. PLoS Comput Biol. 2009 Jun;5(6):e1000406. doi: 10.1371/journal.pcbi.1000406. Epub 2009 Jun 19. PLoS Comput Biol. 2009. PMID: 19543381 Free PMC article.
PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure.
Boomsma W, Frellsen J, Harder T, Bottaro S, Johansson KE, Tian P, Stovgaard K, Andreetta C, Olsson S, Valentin JB, Antonov LD, Christensen AS, Borg M, Jensen JH, Lindorff-Larsen K, Ferkinghoff-Borg J, Hamelryck T. Boomsma W, et al. Among authors: hamelryck t. J Comput Chem. 2013 Jul 15;34(19):1697-705. doi: 10.1002/jcc.23292. Epub 2013 Apr 26. J Comput Chem. 2013. PMID: 23619610
A generative, probabilistic model of local protein structure.
Boomsma W, Mardia KV, Taylor CC, Ferkinghoff-Borg J, Krogh A, Hamelryck T. Boomsma W, et al. Among authors: hamelryck t. Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):8932-7. doi: 10.1073/pnas.0801715105. Epub 2008 Jun 25. Proc Natl Acad Sci U S A. 2008. PMID: 18579771 Free PMC article.
An efficient null model for conformational fluctuations in proteins.
Harder T, Borg M, Bottaro S, Boomsma W, Olsson S, Ferkinghoff-Borg J, Hamelryck T. Harder T, et al. Among authors: hamelryck t. Structure. 2012 Jun 6;20(6):1028-39. doi: 10.1016/j.str.2012.03.020. Epub 2012 May 10. Structure. 2012. PMID: 22578545 Free article.
A Generative Angular Model of Protein Structure Evolution.
Golden M, García-Portugués E, Sørensen M, Mardia KV, Hamelryck T, Hein J. Golden M, et al. Among authors: hamelryck t. Mol Biol Evol. 2017 Aug 1;34(8):2085-2100. doi: 10.1093/molbev/msx137. Mol Biol Evol. 2017. PMID: 28453724 Free PMC article.
48 results