Bringing folding pathways into strand pairing prediction

Authors:
Jieun K. Jeong;Piotr Berman;Teresa M. Przytycka
Affiliations:
Computer Science and Engineering Department, The Pennsylvania State University, University Park, PA and National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD;Computer Science and Engineering Department, The Pennsylvania State University, University Park, PA;National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD
Venue:
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
Year:
2007

Citing 2
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Abstract

The topology of β-sheets is defined by the pattern of hydrogen-bonded strand pairing. Therefore, predicting hydrogen bonded strand partners is a fundamental step towards predicting β-sheet topology. In this work we report a new strand pairing algorithm. Our algorithm attempts to mimic elements of the folding process. Namely, in addition to ensuring that the predicted hydrogen bonded strand pairs satisfy basic global consistency constraints, it takes into account hypothetical folding pathways. Consistently with this view, introducing hydrogen bonds between a pair of strands changes the probabilities of forming other strand pairs. We demonstrate that this approach provides an improvement over previously proposed algorithms.