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Title: biojava-tutorial/structure/alignment.md at biojava-3 · ZeroDesigner/biojava-tutorial · GitHub

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Description: :book::books:An introductory tutorial for BioJava. Contribute to ZeroDesigner/biojava-tutorial development by creating an account on GitHub.

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https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/alignment.md#what-is-a-structure-alignment
protein structure alignmenthttp://en.wikipedia.org/wiki/Structural_alignment
https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/alignment.md#alignment-algorithms-supported-by-biojava
StructureAlignmentFactoryhttp://www.biojava.org/docs/api/org/biojava/bio/structure/align/StructureAlignmentFactory.html
https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/alignment.md#alignment-user-interface
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https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/alignment.md#the-alignment-algorithms
https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/alignment.md#combinatorial-extension-ce
Shindyalov and Bourne in 1998http://peds.oxfordjournals.org/content/11/9/739.short
http://www.ncbi.nlm.nih.gov/pubmed/9796821
SCOP or CATH databaseshttps://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/externaldb.md
Protein Domain Parserhttp://www.biojava.org/docs/api/org/biojava/bio/structure/domain/LocalProteinDomainParser.html
org.biojava.bio.structure.align.ce.CeMainhttp://www.biojava.org/docs/api/org/biojava/bio/structure/align/ce/CeMain.html
https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/alignment.md#combinatorial-extension-with-circular-permutation-ce-cp
Wikipediahttp://en.wikipedia.org/wiki/Circular_permutation_in_proteins
Molecule of the Monthhttp://www.pdb.org/pdb/101/motm.do?momID=124&evtc=Suggest&evta=Moleculeof%20the%20Month&evtl=TopBar
http://www.ncbi.nlm.nih.gov/pubmed/22496628
https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/img/3cna.A_2pel.A_cecp.png
org.biojava.bio.structure.align.ce.CeCPMainhttp://www.biojava.org/docs/api/org/biojava/bio/structure/align/ce/CeCPMain.html
https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/alignment.md#fatcat---rigid
Yuzhen Ye & Adam Godzik in 2003http://bioinformatics.oxfordjournals.org/content/19/suppl_2/ii246.abstract
http://www.ncbi.nlm.nih.gov/pubmed/14534198
org.biojava.bio.structure.align.fatcat.FatCatRigidhttps://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/www.biojava.org/docs/api/org/biojava/bio/structure/align/fatcat/FatCatRigid.html
https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/alignment.md#fatcat---flexible
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org.biojava.bio.structure.align.fatcat.FatCatFlexiblehttps://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/www.biojava.org/docs/api/org/biojava/bio/structure/align/fatcat/FatCatFlexible.html
https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/alignment.md#smith-waterman
http://www.ncbi.nlm.nih.gov/pubmed/7265238
org.biojava.bio.structure.align.ce.CeCPMainhttp://www.biojava.org/docs/api/org/biojava/bio/structure/align/ce/CeCPMain.html
https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/alignment.md#other-methods
BioJavaStructureAlignmenthttp://www.biojava.org/docs/api/org/biojava/bio/structure/align/BioJavaStructureAlignment.html
CeSideChainMainhttp://www.biojava.org/docs/api/org/biojava/bio/structure/align/ce/CeSideChainMain.html
OptimalCECPMainhttp://www.biojava.org/docs/api/org/biojava/bio/structure/align/ce/OptimalCECPMain.html
StructureAlignmenthttp://www.biojava.org/docs/api/org/biojava/bio/structure/align/StructureAlignment.html
https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/alignment.md#pdb-wide-database-searches
herehttp://www.rcsb.org/pdb/static.do?p=general_information/cluster/structureAll.jsp
https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/img/database_search.png
https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/img/database_search_results.png
FATCAT-rigidhttp://www.rcsb.org/pdb/static.do?p=general_information/cluster/structureAll.jsp
DALIhttp://ekhidna.biocenter.helsinki.fi/dali/start
https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/alignment.md#creating-alignments-programmatically
https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/alignment.md#command-line-tools
CE and FATCAThttp://source.rcsb.org/jfatcatserver/download.jsp
https://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/alignment.md#acknowledgements
Homehttps://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/README.md
Book 3: The Protein Structure moduleshttps://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/README.md
Chapter 7 : SEQRES and ATOM recordshttps://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/seqres.md
Chapter 9 : Biological Assemblieshttps://github.com/ZeroDesigner/biojava-tutorial/blob/biojava-3/structure/bioassembly.md
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