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Combinatorial model for sequence and spatial motif discovery in short sequence fragments: examples from beta-barrel membrane proteins.

ABSTRACT: Motifs are over-represented sequence or spatial patterns appearing in proteins. They often play important roles in maintaining protein stability and in facilitating protein functions. When motifs are located in short sequence fragments, as in transmembrane domains that are only 10-20 residues in length, and when there is only very limited data, it is difficult to identify motifs. In this study, we develop combinatorial models for assessing statistically significant sequence and spatial patterns. We show our method can uncover previously unknown sequence and spatial motifs in beta-barrel membrane proteins.

SUBMITTER: Jackups R

PROVIDER: S-EPMC2703457 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature

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Combinatorial model for sequence and spatial motif discovery in short sequence fragments: examples from beta-barrel membrane proteins.

Jackups Ronald R Liang Jie J

Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference 20060101

Motifs are over-represented sequence or spatial patterns appearing in proteins. They often play important roles in maintaining protein stability and in facilitating protein functions. When motifs are located in short sequence fragments, as in transmembrane domains that are only 10-20 residues in length, and when there is only very limited data, it is difficult to identify motifs. In this study, we develop combinatorial models for assessing statistically significant sequence and spatial patterns. ...[more]

PMID: 17947032

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