ArticleProtein science : a publication of the Protein Society2003
Beta edge strands in protein structure prediction and aggregation.
Article in Protein science : a publication of the Protein Society, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
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- β-Bulges: extensive structural analyses of β-sheets irregularities.Protein science : a publication of the Protein Society · 2013Article
- Molecular mechanism by which surface antigen HP0197 mediates host cell attachment in the pathogenic bacteria Streptococcus suis.The Journal of biological chemistry · 2013Article
- A method to predict edge strands in beta-sheets from protein sequences.Computational and structural biotechnology journal · 2013Article
- Coupling of aggregation and immunogenicity in biotherapeutics: T- and B-cell immune epitopes may contain aggregation-prone regions.Pharmaceutical research · 2011Article
- Structural and functional studies of truncated hemolysin A from Proteus mirabilis.The Journal of biological chemistry · 2009Article
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- Characterization of non-trivial neighborhood fold constraints from protein sequences using generalized topohydrophobicity.Bioinformatics and biology insights · 2008Article
- A beta-hairpin comprising the nuclear localization sequence sustains the self-associated states of nucleosome assembly protein 1.Journal of molecular biology · 2008Article
- PPT-DB: the protein property prediction and testing database.Nucleic acids research · 2008Article
- An automated high-throughput screening method for the identification of high-yield, soluble protein variants using cell-free expression and systematic truncation.Journal of structural and functional genomics · 2006Article
- An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements.Protein science : a publication of the Protein Society · 2006Article
- Prediction of beta-strand packing interactions using the signature product.Journal of molecular modeling · 2006Article
- Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs.Protein science : a publication of the Protein Society · 2005Article
- Article
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3 authors.
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Abstract
It is well established that recognition between exposed edges of beta-sheets is an important mode of protein-protein interaction and can have pathological consequences; for instance, it has been linked to the aggregation of proteins into a fibrillar structure, which is associated with a number of predominantly neurodegenerative disorders. A number of protective mechanisms have evolved in the edge strands of beta-sheets, preventing the aggregation and insolubility of most natural beta-sheet proteins. Such mechanisms are unfavorable in the interior of a beta-sheet. The problem of distinguishing edge strands from central strands based on sequence information alone is important in predicting residues and mutations likely to be involved in aggregation, and is also a first step in predicting folding topology. Here we report support vector machine (SVM) and decision tree methods developed to classify edge strands from central strands in a representative set of protein domains. Interestingly, rules generated by the decision tree method are in close agreement with our knowledge of protein structure and are potentially useful in a number of different biological applications. When trained on strands from proteins of known structure, using structure-based (Dictionary of Secondary Structure in Proteins) strand assignments, both methods achieved mean cross-validated, prediction accuracies of approximately 78%. These accuracies were reduced when strand assignments from secondary structure prediction were used. Further investigation of this effect revealed that it could be explained by a significant reduction in the accuracy of standard secondary structure prediction methods for edge strands, in comparison with central strands.
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