FRETView

FRETView is an attempt to develop a Java-based program to reduce much of the complexity involved in obtaining FRET parameters for various donor/acceptor systems. It integrates many of the equations used for doing FRET calculations with a database of commercially available (predominantly from Invitrogen) and user defined chromophores. Currently, it's being developed as a plugin for the InstruView program in order to make it easier to import spectral data and reduce programing complexity, but since it is an open-source program (Download Source Code) it can be modified to run as a standalone program.

Download and Installation

Since FRETView is written as a plugin for the InstruView program (Download InstruView) it requires installation of this program.in order to run. Please follow the instructions below to install and run the program. More detailed installation instructions can be found here.

Make sure you have the latest version of the Java Runtime Environment installed. On Mac OS X this is installed by default.
On Windows, unpack the instruview.zip file in the "C:\" folder. There should now be a folder named C:\InstruView. Change into the installation folder then double click on the instruview.bat file. This should run the program.
On Mac OS X, unpack the instruview.zip file and move the "InstruView" folder to the "Applications" folder on the hardrive. Change into the installation folder then double click on the instruview-mac.command file. This should run the program.
On Linux or Solaris, unpack the instruview.zip file in a convenient location. Change to the "InstruView" directory and edit the "IVHOME" variable in the "instruview" shell script. This variable should point to the directory were the program was unpacked. Run the program by typing "instruview" (no quotes) in the command line.
Once the program is installed and running, please review the help manual which can be found here,or within the program. Any questions or suggestions feel free to contact Nathan (ns2375@columbia.edu).

FRETView in Action

Here are a few screenshots highliting some of the key features of the program. The help manual provides a more detailed overview of the program features.

Figure 1. The main program window showing the simple and intuitive user interface. Anyone familiar with FRET
calculation should find it relatively easy to use the program.

manage tab

Figure 2. The interface used to manage the spectral database. As can be seen, it provides a simple means to manage
a spectral database of donors and acceptors including the ability to download a database from a webserver.

Efficiency Plot

Figure 3. Plot showing the energy transfer efficiency and intensity variation of the donor (Fd), acceptor (Fa)
and total intensity (Ft) as a function of donor/acceptor distance while exciting at 490 nm.

Figure 4. Plot of the simulated spectra when the donor (Alexa 488) and acceptor (Alexa 546) are ~ 70 Å
apart and the excitation wavelength is 490 nm. This distance can be easily varied by moving the slider bar.
The simulation only takes into account energy transfer so it will likely differ from experimental results if
any other photophysical effects are taking place.

Figure 5. Plot of the simulated decay profiles when a long-lived donor, Ru(phen)₃ undergoes energy transfer
with the short-lived acceptor acceptor, Cy5. As can be seen, the lifetime of the acceptor is increased
significantly as a result of the energy transfer process. The lifetime of Cy5 is normally only a few nanoseconds.