TY - GEN
T1 - Bringing folding pathways into strand pairing prediction
AU - Jeong, Jieun K.
AU - Berman, Piotr
AU - Przytycka, Teresa M.
PY - 2007/1/1
Y1 - 2007/1/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=37249010577&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=37249010577&partnerID=8YFLogxK
U2 - 10.1007/978-3-540-74126-8_5
DO - 10.1007/978-3-540-74126-8_5
M3 - Conference contribution
AN - SCOPUS:37249010577
SN - 9783540741251
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 38
EP - 48
BT - Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings
PB - Springer Verlag
T2 - 7th International Workshop on Algorithms in Bioinformatics, WABI 2007
Y2 - 8 September 2007 through 9 September 2007
ER -