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lines changed Original file line number Diff line number Diff line change @@ -59,7 +59,7 @@ algorithms.
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The Combinatorial Extension (CE) algorithm was originally developed by
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[ Shindyalov and Bourne in
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- 1998] ( http://peds.oxfordjournals.org/content/11/9/739.short ) [ ![ Version ] ( http://img.shields.io/badge/in-pubmed-blue.svg?style=flat )] ( http://www.ncbi.nlm.nih.gov/pubmed/9796821 ) .
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+ 1998] ( http://peds.oxfordjournals.org/content/11/9/739.short ) [ ![ pubmed ] ( http://img.shields.io/badge/in-pubmed-blue.svg?style=flat )] ( http://www.ncbi.nlm.nih.gov/pubmed/9796821 ) .
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It works by identifying segments of the two proteins with similar local
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structure, and then combining those to try to align the most residues possible
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while keeping the overall RMSD of the superposition low.
@@ -103,7 +103,8 @@ BioJava class: [org.biojava.bio.structure.align.ce.CeCPMain](http://www.biojava.
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This is a Java implementation of the original FATCAT algorithm by [ Yuzhen Ye
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& ; Adam Godzik in
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- 2003] ( http://bioinformatics.oxfordjournals.org/content/19/suppl_2/ii246.abstract ) .
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+ 2003] ( http://bioinformatics.oxfordjournals.org/content/19/suppl_2/ii246.abstract )
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+ [ ![ pubmed] ( http://img.shields.io/badge/in-pubmed-blue.svg?style=flat )] ( http://www.ncbi.nlm.nih.gov/pubmed/14534198 ) .
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It performs similarly to CE for most proteins. The 'rigid' flavor uses a
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rigid-body superposition and only considers alignments with matching sequence
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order.
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