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Figure 1 | BMC Bioinformatics

Figure 1

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

Figure 1

Protocol used in this study. Non redundant protein structures were simplified using the structural alphabet HMM-SA and structural motifs extracted using the protocol presented in Figure 2. Over-represented structural motifs in SCOP superfamilies in protein loops were detected using the SPatt software. Based on SPatt statistics, two types of words were distinguished: ubiquitous words, over-represented in several superfamilies, and superfamily-specific words, over-represented in few superfamilies. Some ubiquitous words were compared with known structural motifs: β-turns identified by the ExtractTurn software and structural motifs presented in the Motivated Proteins database. Some superfamily-specific words were compared with functional sites, using Swiss-Prot annotations and external softwares.

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BMC Bioinformatics

ISSN: 1471-2105

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