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Type PDB code of two proteins to compare
(on the next page you will be able to choose a protein chain if available)
First Protein:  (1ggg)
Second Protein:  (1hpb)
Maximal RMSD between matched fragments
Minimal size of matched fragments (Num. of Amino Acids)

FlexProt Download (for Linux OS only) Flexible Protein Structure Alignment

What is FlexProt? :

FlexProt detects the optimal flexible structural alignment of a pair of protein structures. The first structure is assumed to be rigid, while in the second structure potential flexible regions are automatically detected.
"Flexible protein alignment and hinge detection", M. Shatsky, H.J. Wolfson, and R. Nussinov, Proteins: Structure, Function, and Genetics 48:242-256, 2002.

For comments : max.shatsky@gmail.com