Bringing folding pathways into strand pairing prediction

Jieun K. Jeong; Piotr Berman; Teresa M. Przytycka

doi:10.1007/978-3-540-74126-8_5

Bringing folding pathways into strand pairing prediction

Jieun K. Jeong, Piotr Berman, Teresa M. Przytycka

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

7 Scopus citations

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.

Original language	English (US)
Title of host publication	Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings
Publisher	Springer Verlag
Pages	38-48
Number of pages	11
ISBN (Print)	9783540741251
DOIs	https://doi.org/10.1007/978-3-540-74126-8_5
State	Published - Jan 1 2007
Event	7th International Workshop on Algorithms in Bioinformatics, WABI 2007 - PhiIadelphia, PA, United States Duration: Sep 8 2007 → Sep 9 2007

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	4645 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	7th International Workshop on Algorithms in Bioinformatics, WABI 2007
Country	United States
City	PhiIadelphia, PA
Period	9/8/07 → 9/9/07

All Science Journal Classification (ASJC) codes

Theoretical Computer Science
Computer Science(all)

Access to Document

10.1007/978-3-540-74126-8_5

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Jeong, J. K., Berman, P., & Przytycka, T. M. (2007). Bringing folding pathways into strand pairing prediction. In Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings (pp. 38-48). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4645 LNBI). Springer Verlag. https://doi.org/10.1007/978-3-540-74126-8_5

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Jeong, JK, Berman, P & Przytycka, TM 2007, Bringing folding pathways into strand pairing prediction. in Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 4645 LNBI, Springer Verlag, pp. 38-48, 7th International Workshop on Algorithms in Bioinformatics, WABI 2007, PhiIadelphia, PA, United States, 9/8/07. https://doi.org/10.1007/978-3-540-74126-8_5

Bringing folding pathways into strand pairing prediction. / Jeong, Jieun K.; Berman, Piotr; Przytycka, Teresa M.

Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings. Springer Verlag, 2007. p. 38-48 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 4645 LNBI).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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Jeong JK, Berman P, Przytycka TM. Bringing folding pathways into strand pairing prediction. In Algorithms in Bioinformatics - 7th International Workshop, WABI 2007, Proceedings. Springer Verlag. 2007. p. 38-48. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-540-74126-8_5