References#
Ronny Lorenz, Stephan H. Bernhart, Christian Höner Zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, and Ivo L. Hofacker. Viennarna package 2.0. Algorithms for molecular biology, 6(1):26, 2011. doi:10.1073/pnas.1114859109https://doi.org/10.1021/bi201420a.
Andrew Martin Watkins, Ramya Rangan, and Rhiju Das. Farfar2: improved de novo rosetta prediction of complex global rna folds. Structure, 28(8):963–976.e6, 2020. doi:10.1016/j.str.2020.05.011.
Fabio D. Steffen, Roland K. O. Sigel, and Richard Börner. Fretraj: integrating single-molecule spectroscopy with molecular dynamics. Bioinformatics, 21:3953–3955, 2021. doi:10.1093/bioinformatics/btab615.
Fabio D. Steffen, Roland K. O. Sigel, and Richard Börner. An atomistic view on carbocyanine photophysics in the realm of rna. Physical chemistry chemical physics, 18(42):29045–29055, 2016. doi:10.1039/c6cp04277e.
Mykola Dimura, Thomas-Otavio Peulen, Christian A. Hanke, Aiswaria Prakash, Holger Gohlke, and Claus A. M. Seidel. Quantitative fret studies and integrative modeling unravel the structure and dynamics of biomolecular systems. Current Opinion in Structural Biology, 40:163–185, 2016. doi:10.1016/j.sbi.2016.11.012.
Martin Hoefling, Nicola Lima, Dominik Haenni, Claus A. M. Seidel, Benjamin Schuler, and Helmut Grubmüller. Structural heterogeneity and quantitative fret efficiency distributions of polyprolines through a hybrid atomistic simulation and monte carlo approach. PLoS ONE, 6(5):e19791, 2011. doi:10.1371/journal.pone.0019791.
Mark James Abraham, Teemu Murtola, Roland Schulz, Szilárd Páll, Jeremy C. Smith, Berk Hess, and Erik Lindahl. Gromacs: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2:19–25, 2015. doi:10.1016/j.softx.2015.06.001.
Martin Hoefling and Helmut Grubmüller. In silico fret from simulated dye dynamics. Computer Physics Communications, 184(3):841–852, 2013. doi:10.1016/j.cpc.2012.10.018.