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* Bourne PE, Shindyalov IN. (2003): ''Structure Comparison and Alignment''. In: Bourne, P.E., Weissig, H. (Eds): ''Structural Bioinformatics''. Hoboken NJ: Wiley-Liss. {{ISBN|0-471-20200-2}}
* 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
* {{cite journal |vauthors=Ye Y, Godzik A | year = 2005 | title = Multiple flexible structure alignment using partial order graphs | url = http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/10/2362 | journal = Bioinformatics | volume = 21 | issue = 10| pages = 2362–2369 | doi=10.1093/bioinformatics/bti353| pmid = 15746292 | doi-access = free }}
* {{cite journal |vauthors=Sippl M, Wiederstein M | year = 2008 | title = A note on difficult structure alignment problems | url = http://bioinformatics.oxfordjournals.org/cgi/content/full/24/3/426?ijkey=oWkOpf10zxhKaF2&keytype=ref | journal = Bioinformatics | volume = 24 | issue = 3| pages = 426–427 | doi=10.1093/bioinformatics/btm622| pmid = 18174182 | doi-access = free }}
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