There are various was to configure security on NT/2000 that are compatible with PR-Tracker operation. PR-Tracker Web Client supports Anonymous Access, Basic Authentication, NT Challenge/Response and secure https protocol. Security controlled by IIS and NTFS Access Control List settings on PRTRACKERDB.
Configuring virtual directory security with IIS 4.0
Configuring virtual directory security with IIS 5.0
Setting PRTRACKERDB security on Windows NT 4.0