Is there a way for PROSPECT 1.0/1.1 to analyze and overlay 3-D structural similarities between proteins of similar types?
Rasmol / RasTop can give more accurate and detailed information. However, it must be emphasized that PROSPECT is a structure *prediction* program, rather than a structure *analysis* tool. It bridges between the amino acid sequence and the possible structure, but it doesn’t tell you too much about the structure since it’s not the focus of the software. There is a tool called Swiss-Pdb Viewer (http://us.expasy.org/spdbv/mainpage.html) that does it. There is another utility called DALI, which is an online server that does structure analysis for a submitted pdb file. It’s free to academics.
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