Cn3D

Cn3D is a Windows, Macintosh and Unix-based software from the United States National Library of Medicine that acts as a helper application for web browsers to view three-dimensional structures from The National Center for Biotechnology Information's Entrez retrieval service. It "simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features", according to its official site. Cn3D is in public domain with source code available.