DICE (Dimensional Inferences from Coarse-grained Ensembles)
The DICE web tool computes the radius of gyration, \(R_g\), of disordered or denatured peptide chains based on single-molecule FRET data and an unbiased homopolymer model. In the direct mode, the output is either the most likely \(R_g\) value (\( R_g^0 \)) or a distribution of \(R_g\) values that is consistent with the experimental FRET efficiency (E), which can be input either as a single value (mean) or as a distribution of E. In the reverse mode, the program estimates the expected FRET efficiency and the distribution of \(R_g\) based on a distribution of end-to-end distances; for example derived from coarse-grained simulations, an analytical expression, or from Protein Ensemble Database (pE-DB) conformations. For more details, see Song, Gomes, Shi, Gradinaru & Chan, Biophys. J. (2017), and Song, Gomes, Gradinaru & Chan, J. Phys. Chem. B (2015).