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Figure 2 | BMC Bioinformatics

Figure 2

From: Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

Figure 2

Protocol used for extraction of structural motifs. A: the 27 structural letters of HMM-SA. B: input 3D structure. C: sequence of structural letters resulting from the simplification. D: extraction of loops based on regular expressions of structural letters; the geometry of a loop encoded by SPBDRPI is shown on the right side. E: systematic splitting of loops into overlapping words of four consecutive structural letters. The geometry of two structural words, KGDR and DRPI, are shown with superimposition of their fragments. Fragments are superimposed with ProFit software http://www.bioinf.org.uk/software/profit and represented with Pymol http://www.pymol.org.

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BMC Bioinformatics

ISSN: 1471-2105

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