MODELLER is available free of charge to academic non-profit institutions (you will, however, need to register for a license).
For commercial entities or government research labs (such as the NIH and national labs in the USA), MODELLER is available from BIOVIA (formerly Accelrys). For further details, please contact BIOVIA at 5005 Wateridge Vista Drive, San Diego, CA 92121, USA, Tel: +1 858 799 5000, email firstname.lastname@example.org or via their contact form.
Accelrys also makes commercially available several graphical interfaces to MODELLER. Teaching licenses are available to those institutions that acquire and maintain a research license.