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* Yuan X, Bystroff C. (2004) "Non-sequential Structure-based Alignments Reveal Topology-independent Core Packing Arrangements in Proteins", ''Bioinformatics''. Nov 5, 2004
* {{cite journal |vauthors=Jung J, Lee B | year = 2000 | title = Protein structure alignment using environmental profiles | journal = Protein Eng | volume = 13 | issue = 8| pages = 535–543 | doi=10.1093/protein/13.8.535| doi-access = free }}
* {{cite journal |vauthors=Ye Y, Godzik A | year = 2005 | title = Multiple flexible structure alignment using partial order graphs
* {{cite journal |vauthors=Sippl M, Wiederstein M | year = 2008 | title = A note on difficult structure alignment problems
{{Protein methods}}
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