Bringing Folding Pathways into Strand Pairing Prediction

Abstract. The topology of β-sheets is defined by the pattern of hydrogenbonded 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.

• Type: Conference
• Year: 2007
• Where: WABI
• Authors: Jieun K. Jeong, Piotr Berman, Teresa M. Przytycka
• Keywords: Algorithms, Strand Pairing, Strand Pairing Algorithm, Strand Pairs, WABI 2007