Editing Structural alignment (section)

==References==
{{reflist|35em|refs=
<ref name="Bartheletal">{{cite journal|author=Barthel D., Hirst J.D., Blazewicz J., Burke E.K. and Krasnogor N.|year= 2007|title= ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information|journal=BMC Bioinformatics|volume= 8|pages=416|doi=10.1186/1471-2105-8-416|pmid=17963510|pmc=2222653|doi-access= free}}</ref>

<ref name="cech">{{cite journal|vauthors=Cech P, Svozil D, Hoksza D |year=2012|title= SETTER: web server for RNA structure comparison|journal=Nucleic Acids Research|volume= 40|issue=W1|pages=W42–W48|doi=10.1093/nar/gks560|pmid=22693209|pmc=3394248}}</ref>

<ref name="Diederichs">{{cite journal|author=Diederichs K. |year=1995|title= Structural superposition of proteins with unknown alignment and detection of topological similarity using a six-dimensional search algorithm|journal=Proteins|volume= 23|issue=2|pages=187–95|doi=10.1002/prot.340230208|pmid=8592700|s2cid=3469775|url=http://nbn-resolving.de/urn:nbn:de:bsz:352-opus-40461}}</ref>

<ref name="fischer">{{cite journal|vauthors=Siew N, Elofsson A, Rychlewsk L, Fischer D |year=2000|title= MaxSub: an automated measure for the assessment of protein structure prediction quality|journal=Bioinformatics|volume= 16|pages=776–85|doi=10.1093/bioinformatics/16.9.776|pmid=11108700|issue=9|doi-access=free}}</ref>

<ref name="godzik">{{cite journal|author=Godzik A|pmid=8819165|year=1996|title=The structural alignment between two proteins: Is there a unique answer?|volume=5|issue=7|pages=1325–38|pmc=2143456|doi=10.1002/pro.5560050711|journal=Protein Science}}</ref>

<ref name="havgaard">{{cite journal|vauthors=Havgaard JH, Lyngso RB, Stormo GD, Gorodkin J |year=2005|title= Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%|journal=Bioinformatics|volume= 21|issue=9|pages=1815–24|doi=10.1093/bioinformatics/bti279|pmid=15657094|doi-access=free}}</ref>

<ref name="hoksza">{{cite journal|vauthors=Hoksza D, Svozil D |year=2012|title= Efficient RNA pairwise structure comparison by SETTER method|journal=Bioinformatics|volume= 28|issue=14|pages=1858–1864|doi=10.1093/bioinformatics/bts301|pmid=22611129|url=https://zenodo.org/record/890287|doi-access=free}}</ref>

<ref name="holm">{{cite journal|vauthors=Holm L, Sander C |pmid=8662544|year=1996|title=Mapping the protein universe|volume=273|issue=5275|pages=595–603|journal=Science|doi=10.1126/science.273.5275.595|bibcode=1996Sci...273..595H |s2cid=7509134}}</ref>

<ref name="kolodny">{{cite journal|vauthors=Kolodny R, Linial N |year=2004|title= Approximate protein structural alignment in polynomial time |journal=PNAS|volume= 101|issue=33|pages= 12201–12206|doi=10.1073/pnas.0404383101|pmid=15304646|pmc=514457|doi-access=free}}</ref>

<ref name="lathrop">{{cite journal|author=Lathrop RH. |year=1994|title= The protein threading problem with sequence amino acid interaction preferences is NP-complete|journal=Protein Eng|volume= 7|issue=9|pages=1059–68|doi=10.1093/protein/7.9.1059|pmid=7831276|citeseerx=10.1.1.367.9081}}</ref>

<ref name="lovo1">{{cite journal|author=Martinez L, Andreani, R, Martinez, JM. |year=2007|title= Convergent algorithms for protein structural alignment |journal=BMC Bioinformatics|volume= 8|pages=306|doi=10.1186/1471-2105-8-306|pmid=17714583|pmc=1995224 |doi-access=free }}</ref>

<ref name="Maiti">{{cite journal|author4-link=David S. Wishart|vauthors=Maiti R, Van Domselaar GH, Zhang H, Wishart DS |year=2004|title= SuperPose: a simple server for sophisticated structural superposition|journal=Nucleic Acids Res|volume= 32|pages=W590–4|doi=10.1093/nar/gkh477|pmid=15215457|issue=Web Server issue|pmc=441615}}</ref>

<ref name="martin">{{cite journal|author=Martin ACR|year=1982|title= Rapid Comparison of Protein Structures|journal=Acta Crystallogr A|volume= 38|pages= 871–873|doi=10.1107/S0567739482001806|issue=6|bibcode=1982AcCrA..38..871M }}</ref>

<ref name="Mathews">{{cite journal|vauthors=Mathews DH, Turner DH |year=2006|title= Prediction of RNA secondary structure by free energy minimization|journal=Curr Opin Struct Biol|volume= 16|issue=3|pages=270–8|doi=10.1016/j.sbi.2006.05.010|pmid=16713706}}</ref>

<ref name="orengo">{{cite journal|vauthors=Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM |year=1997|title= CATH: A hierarchical classification of protein domain structures|journal=Structure|volume= 5|issue=8|pages= 1093–1108|doi=10.1016/S0969-2126(97)00260-8|pmid=9309224|doi-access=free}}</ref>

<ref name="poleksic">{{cite journal|author=Poleksic A |year=2009|title= Algorithms for optimal protein structure alignment|journal=Bioinformatics|volume= 25|pages= 2751–2756|doi=10.1093/bioinformatics/btp530|pmid=19734152|issue=21|doi-access=free}}</ref>

<ref name="prlic">{{cite journal|vauthors=Prlic A, Bliven S, Rose PW, Bluhm WF, Bizon C, Godzik A, Bourne PE |year=2010|title= Pre-calculated protein structure alignments at the RCSB PDB website |pmid=20937596|pages= 2983–2985|volume=26|issue=23|doi=10.1093/bioinformatics/btq572|pmc=3003546|journal=Bioinformatics}}</ref>

<ref name="skolnick">{{cite journal|vauthors=Zhang Y, Skolnick J |year=2005|title= The protein structure prediction problem could be solved using the current PDB library|journal= Proc Natl Acad Sci USA|pmid=15653774|doi=10.1073/pnas.0407152101  |volume=102|issue=4|pages=1029–34|pmc=545829|bibcode=2005PNAS..102.1029Z |doi-access=free}}</ref>

<ref name="taylor">{{cite journal|vauthors=Taylor WR, Flores TP, Orengo CA |year=1994|title= Multiple protein structure alignment|journal=Protein Sci|volume= 3|issue=10|pages=1858–70|doi=10.1002/pro.5560031025|pmid=7849601|pmc=2142613}}</ref>

<ref name="theobald">{{cite journal|vauthors=Theobald DL, Wuttke DS |year=2006|title= Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem|journal=Proceedings of the National Academy of Sciences|volume= 103|pages=18521–18527|doi=10.1073/pnas.0508445103|issue=49|pmid=17130458|pmc=1664551|bibcode=2006PNAS..10318521T |doi-access=free}}</ref>

<ref name="theobald2">{{cite journal|vauthors=Theobald DL, Wuttke DS |year=2006|journal=Bioinformatics|volume= 22|pages=2171–2172|doi=10.1093/bioinformatics/btl332|title=THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures|issue=17|pmid=16777907|pmc=2584349}}</ref>

<ref name="Torarinsson">{{cite journal|vauthors=Torarinsson E, Sawera M, Havgaard JH, Fredholm M, Gorodkin J |year=2006|title= Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure|journal=Genome Res|volume= 16|issue=7|pages=885–9|doi=10.1101/gr.5226606|pmid=16751343|pmc=1484455}}</ref>

<ref name="wang">{{cite journal |last1=Wang |first1=Lusheng |last2=Jiang |first2=Tao |title=On the complexity of multiple sequence alignment. |journal=Journal of Computational Biology |date=1994 |volume=1 |issue=4 |pages=337–48 |doi=10.1089/cmb.1994.1.337 |pmid=8790475 |name-list-style=vanc|citeseerx=10.1.1.408.894 }}</ref>

<ref name="zemla">{{cite journal|author=Zemla A. |year=2003|title= LGA — A Method for Finding 3-D Similarities in Protein Structures|journal=Nucleic Acids Research|volume= 31|issue=13|pages=3370–3374|doi=10.1093/nar/gkg571|pmid=12824330|pmc=168977}}</ref>

<ref name="ZhangTMalign">{{cite journal|vauthors=Zhang Y, Skolnick J |year=2005|journal=Nucleic Acids Research|volume= 33|pages= 2302–2309|doi=10.1093/nar/gki524|pmid=15849316|title=TM-align: A protein structure alignment algorithm based on the TM-score|issue=7|pmc=1084323}}</ref>

<ref name="ZhangTMscore">{{cite journal|vauthors=Zhang Y, Skolnick J |year=2004|journal=Proteins|volume= 57|pages= 702–710|doi=10.1002/prot.20264|pmid=15476259|title=Scoring function for automated assessment of protein structure template quality|issue=4|s2cid=7954787}}</ref>

}}

===Further reading===
* 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 | journal = Protein Eng | volume = 13 | issue = 8| pages = 535–543 | doi=10.1093/protein/13.8.535| pmid = 10964982 | doi-access = free }}
* {{cite journal |vauthors=Ye Y, Godzik A | year = 2005 | title = Multiple flexible structure alignment using partial order graphs | 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 | journal = Bioinformatics | volume = 24 | issue = 3| pages = 426–427 | doi=10.1093/bioinformatics/btm622| pmid = 18174182 | doi-access = free }}

{{Protein methods}}

{{DEFAULTSORT:Structural Alignment}}
[[Category:Protein methods]]
[[Category:NP-complete problems]]