Reference: Multiple flexible structure alignment using partial order graphs. Yuzhen Ye and Adam Godzik. Bioinformatics, 2005 21(10):2362-2369 (Sorry for the BW figures in the paper. You can get the color figures 4-6 from here)
Demonstration: See an example; MyPOSA: Retrieve old results
FAQS: POSA alignment output; POSA output visualization; POSA help file

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Provide input protein structures (please no more than 20) by one of the three ways below
(1) Provide PDB codes (codes are seperated by spaces; a code is 4-char-ID + 1-char-chain; use _ for no chain)
for example, 1adjA 1hc7A 1qf6A 1atiA

(2) Provide SCOP codes (codes are seperated by spaces; a code is 6-character-ID)
for example, d1ncx__ d2sas__ d1jfja_

(3) Upload a tar/zip file of your PDB structures [help]