References

Citation

If you use FRETraj in your work please cite the following paper:

F.D. Steffen, R.K.O. Sigel, R. Börner, Bioinformatics 2021, 37, 3953–3955.

The contact volume (CV) as an extension of the accessible volume (AV) was introduced in:

F.D. Steffen, R.K.O. Sigel, R. Börner, Phys. Chem. Chem. Phys 2016, 18, 29045-29055.

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Related projects

The accessible volume (AV) approach is described as a geometrical search based on Djikstra’s algorithm.

• S. Sindbert, S. Kalinin, C.A.M. Seidel et al. JACS, 2011, 133, 2463-2480.

• S. Kalinin, T. Peulen, C.A.M. Seidel et al. Nat. Methods, 2012, 9, 1218-1225.

The nano-positioning system (NPS) uses a Bayesian model to locate the dye with respect to the biomolecule

• A. Muschielok, J. Jawhari, J. Michaelis, Nat. Methods, 2008, 5, 965-971.

• T. Eilert, M. Beckers, F. Drechsler, J. Michaelis, Comput. Phys. Commun., 2017, 219, 377–389.

Review of different dye-linker models including the ACV

• M. Dimura, T. Peulen, C.A.M. Seidel et al. Curr. Opin. Struct. Biol. 2016, 40, 163-185.

• T. Peulen, O. Opanasyuk, C.A.M Seidel, J. Phys. Chem . B., 2017, 121, 8211-8241.

A recent benchmark for FRET-assisted modeling of proteins

• M. Dimura, T. Peulen, C.A.M Seidel et al. Nat. Commun. 2020, 11, 5394.

The Markov-chain based photon simulator was inspired by md2fret

• M. Hoefling, H. Grubmüller, Comput. Phys. Commun. 2013, 184, 841-852.

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Fabio D. Steffen, Roland K. O. Sigel, and Richard Börner. An atomistic view on carbocyanine photophysics in the realm of rna. Phys. Chem. Chem. Phys., 18(42):29045–29055, 2016. doi:10.1039/c6cp04277e.

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