- On Microsoft Windows platforms, the installer adds the ability to open command prompts that setup the user environment to run specific versions of FRED or the latest version of FRED.
- FRED and FRED_RECEPTOR are now versioned and shipped together.
- FRED licenser has been updated to work with licenses that expire past the year 2009.
- The FRED licenser supports having the license file located in the users home directory.
- SD files are now written with the 3D flag set.
- Fixed issue where Fred could crash if -nodock is specified and the poses given to Fred to score are not within the receptor site.