FRETraj is a Python module for predicting FRET efficiencies by calculating multiple accessible-contact volumes (multi-ACV) to estimate donor and acceptor dye dynamics. The package features a user-friendly PyMOL plugin¹ for for FRET-assisted, integrative structural modeling. It interfaces with the LabelLib library for fast computation of ACVs. Specifically, FRETraj is designed to:

• plan (single-molecule) FRET experiments by optimizing labeling positions
• interpret FRET-based distance measurements on a biomolecule
• integrate FRET experiments with molecular dynamics simulations

Follow the instructions for your platform here

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

• F.D. Steffen, R.K.O. Sigel, R. Börner, Bioinformatics 2021.

• F.D. Steffen, R.A. Cunha, R.K.O. Sigel, R. Börner, Nucleic Acids Res. 2024, 52, e59.
• F.D. Steffen, R.K.O. Sigel, R. Börner, Phys. Chem. Chem. Phys. 2016, 18, 29045-29055.
• S. Kalinin, T. Peulen, C.A.M. Seidel et al. Nat. Methods, 2012, 9, 1218-1225.
• T. Eilert, M. Beckers, F. Drechsler, J. Michaelis, Comput. Phys. Commun., 2017, 219, 377–389.
• M. Dimura, T. Peulen, C.A.M. Seidel et al. Curr. Opin. Struct. Biol. 2016, 40, 163-185.
• M. Dimura, T. Peulen, C.A.M Seidel et al. Nat. Commun. 2020, 11, 5394.

¹ PyMOL was developed by WarrenDeLano and is maintained by Schrödinger, LLC.