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Improving descriptions of alignment algorithms
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structure/alignment.md

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@@ -44,20 +44,66 @@ The functionality to perform and visualize these alignments can of course be use
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### Combinatorial Extension (CE)
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The Combinatorial Extension (CE) algorithm was originally developed by [Shindyalov and Bourne in 1998](http://peds.oxfordjournals.org/content/11/9/739.short).
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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).
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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.
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CE is a rigid-body alignment algorithm, which means that the structures being
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compared are kept fixed during superpositon. In some cases it may be desirable
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to break large proteins up into domains prior to aligning them (by manually
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inputing a subrange, using the [SCOP or CATH databases](externaldb.md), or by
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decomposing the protein automatically using the [Protein Domain
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Parser](http://www.biojava.org/docs/api/org/biojava/bio/structure/domain/LocalProteinDomainParser.html)
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algorithm).
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### Combinatorial Extension with Circular Permutation (CE-CP)
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This is a new variation of CE that can detect circular permutations in proteins. @sbliven & @andreasprlic , unpublished
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CE and FATCAT both assume that aligned residues occur in the same order in both
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proteins (e.g. they are both *sequence-order dependent* algorithms). In proteins
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related by a circular permutation, the N-terminal part of one protein is related
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to the C-terminal part of the other, and vice versa. CE-CP allows circularly
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permuted proteins to be compared. For more information on circular
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permutations, see the
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[wikipedia](http://en.wikipedia.org/wiki/Circular_permutation_in_proteins) or
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[Molecule of the
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Month](http://www.pdb.org/pdb/101/motm.do?momID=124&evtc=Suggest&evta=Moleculeof%20the%20Month&evtl=TopBar)
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articles.
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For proteins without a circular permutation, CE-CP results look very similar to
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CE results (with perhaps some minor differences and a slightly longer
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calculation time). If a circular permutation is found, the two halves of the
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proteins will be shown in different colors:
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![Concanavalin A (yellow & orange) aligned with Pea Leptin (blue and cyan)](img/3cna.A_2pel.A_cecp.png)
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CE-CP was developed by Spencer E. Bliven, Philip E. Bourne, and Andreas Prlić.
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### FATCAT - rigid
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This is a Java implementation of the original FATCAT algorithm. [Yuzhen Ye & Adam Godzik in 2003] (http://bioinformatics.oxfordjournals.org/content/19/suppl_2/ii246.abstract)
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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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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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### FATCAT - flexible
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Just as FATCAT - rigid, a Java implementation of the original FATCAT algorithm.
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FATCAT-flexible introduces 'twists' between different parts of the proteins
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which are superimposed independently. This is ideal for proteins which undergo
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large conformational shifts, where a global superposition cannot capture the
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underlying similarity between domains. For instance, the structures of
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calmodulin with and without calcium bound can be much better aligned with
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FATCAT-flexible than with one of the rigid alignment algorithms. The downside of
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this is that it can lead to additional false positives in unrelated structures.
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![(Left) Rigid and (Right) flexible alignments of
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calmodulin](img/1cfd_1cll_fatcat.png)
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## Acknowledgements
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Thanks to P. Bourne, Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute their algorithms.
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Thanks to P. Bourne, Yuzhen Ye and A. Godzik for granting permission to freely use and redistribute their algorithms.

structure/img/1cfd_1cll_fatcat.png

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structure/img/1cfd_1cll_flexible.png

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structure/img/1cfd_1cll_rigid.png

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structure/img/3cna.A_2pel.A_cecp.png

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