Compare3D is used to analyze the structure alignment of two or more polypeptide chains. The alignment is provided by the user, and is thus designed as a visual front end to another program.Compare3D applet uses temporary POM (Property Object Model) database generated in user specified scratch directory. This database contain 3D structure and alignment information provided by user as files in PDB format and alignment information.
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Shindyalov IN, Bourne PE.
A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm.
Nucleic Acids Res. 2001 Jan 1;29(1):228-9.