Program description
The purpose of the software QUEST (QUenching ESTimation) is to simulate dynamic quenching of xanthene dyes tethers to proteins by flexible linkers by simulating PET and the diffusion of dyes. In QUEST the dyes are approximated by a sphere diffusing within their accessible volume (AV). The quenching by PET of MET, PRO, TYR and TRP residues is approximated by a step function where the dye is quenched with a provided rate contestant if it is closer than a given threshold distance. Fig. 1 (shown below) presents the interface of QUEST. The Interface is separated into an input/output region (1, to the left) and an output region (2 and 3, to the right). The relevant simulations parameters are set in the region to the left. The simulations results are shown in the region to right. The simulation parameters are briefly listed an explained on the parameter page.
The interface of QUEST (1) Input parameters (2) graphical representation of the simulated Brownian dynamics trajectory. The distance between the current position and the average position of the entire trajectory is displayed independence of the simulation time (3) autocorrelation of the trajectory shown in (2)