>Is there / is anyone aware of a program that can recognize structurally
>conserved regions in proteins? The input should be something like two
See this recent mini-review for programs and pointers:
Holm, L.; Sander, C. "Searching Protein Structure Databases has Come
of Age" Proteins 1994, 19, 165-173.
It have the info you need and get you started.
Res. Asst. Prof.
Dept. of Medicinal Chemistry
Medical College of Virginia / Virginia Commonwealth Univ.