Protein folding and chart parsing

Julia Hockenmaier; Aravind K. Joshi; Ken A. Dill

doi:10.3115/1610075.1610117

Protein folding and chart parsing

Julia Hockenmaier
, Aravind K. Joshi
, Ken A. Dill

Laufer Center for Physical and Quantitative Biology

Stony Brook University

University of Pennsylvania

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

1 Scopus citations

Abstract

How can proteins fold so quickly into their unique native structures? We show here that there is a natural analogy between parsing and the protein folding problem, and demonstrate that CKY can find the native structures of a simplified lattice model of proteins with high accuracy.

Original language	English
Title of host publication	COLING/ACL 2006 - EMNLP 2006
Subtitle of host publication	2006 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference
Publisher	Association for Computational Linguistics (ACL)
Pages	293-300
Number of pages	8
ISBN (Print)	1932432736, 9781932432732
DOIs	https://doi.org/10.3115/1610075.1610117
State	Published - 2006
Event	11th Conference on Empirical Methods in Natural Language Proceessing, EMNLP 2006, Held in Conjunction with COLING/ACL 2006 - Sydney, NSW, Australia Duration: Jul 22 2006 → Jul 23 2006

Publication series

Name	COLING/ACL 2006 - EMNLP 2006: 2006 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference

Conference

Conference	11th Conference on Empirical Methods in Natural Language Proceessing, EMNLP 2006, Held in Conjunction with COLING/ACL 2006
Country/Territory	Australia
City	Sydney, NSW
Period	07/22/06 → 07/23/06

Access to Document

10.3115/1610075.1610117

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Hockenmaier, J., Joshi, A. K., & Dill, K. A. (2006). Protein folding and chart parsing. In COLING/ACL 2006 - EMNLP 2006: 2006 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference (pp. 293-300). (COLING/ACL 2006 - EMNLP 2006: 2006 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference). Association for Computational Linguistics (ACL). https://doi.org/10.3115/1610075.1610117

Hockenmaier, Julia ; Joshi, Aravind K. ; Dill, Ken A. / Protein folding and chart parsing. COLING/ACL 2006 - EMNLP 2006: 2006 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference. Association for Computational Linguistics (ACL), 2006. pp. 293-300 (COLING/ACL 2006 - EMNLP 2006: 2006 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference).

@inproceedings{86437ef74c0345bdb9ab2acc3a32c3e8,

title = "Protein folding and chart parsing",

abstract = "How can proteins fold so quickly into their unique native structures? We show here that there is a natural analogy between parsing and the protein folding problem, and demonstrate that CKY can find the native structures of a simplified lattice model of proteins with high accuracy.",

author = "Julia Hockenmaier and Joshi, \{Aravind K.\} and Dill, \{Ken A.\}",

year = "2006",

doi = "10.3115/1610075.1610117",

language = "English",

isbn = "1932432736",

series = "COLING/ACL 2006 - EMNLP 2006: 2006 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference",

publisher = "Association for Computational Linguistics (ACL)",

pages = "293--300",

booktitle = "COLING/ACL 2006 - EMNLP 2006",

note = "11th Conference on Empirical Methods in Natural Language Proceessing, EMNLP 2006, Held in Conjunction with COLING/ACL 2006 ; Conference date: 22-07-2006 Through 23-07-2006",

}

Hockenmaier, J, Joshi, AK & Dill, KA 2006, Protein folding and chart parsing. in COLING/ACL 2006 - EMNLP 2006: 2006 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference. COLING/ACL 2006 - EMNLP 2006: 2006 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference, Association for Computational Linguistics (ACL), pp. 293-300, 11th Conference on Empirical Methods in Natural Language Proceessing, EMNLP 2006, Held in Conjunction with COLING/ACL 2006, Sydney, NSW, Australia, 07/22/06. https://doi.org/10.3115/1610075.1610117

Protein folding and chart parsing. / Hockenmaier, Julia; Joshi, Aravind K.; Dill, Ken A.
COLING/ACL 2006 - EMNLP 2006: 2006 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference. Association for Computational Linguistics (ACL), 2006. p. 293-300 (COLING/ACL 2006 - EMNLP 2006: 2006 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference).

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

TY - GEN

T1 - Protein folding and chart parsing

AU - Hockenmaier, Julia

AU - Joshi, Aravind K.

AU - Dill, Ken A.

PY - 2006

Y1 - 2006

N2 - How can proteins fold so quickly into their unique native structures? We show here that there is a natural analogy between parsing and the protein folding problem, and demonstrate that CKY can find the native structures of a simplified lattice model of proteins with high accuracy.

AB - How can proteins fold so quickly into their unique native structures? We show here that there is a natural analogy between parsing and the protein folding problem, and demonstrate that CKY can find the native structures of a simplified lattice model of proteins with high accuracy.

UR - https://www.scopus.com/pages/publications/80053342881

U2 - 10.3115/1610075.1610117

DO - 10.3115/1610075.1610117

M3 - Conference contribution

SN - 1932432736

SN - 9781932432732

T3 - COLING/ACL 2006 - EMNLP 2006: 2006 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference

SP - 293

EP - 300

BT - COLING/ACL 2006 - EMNLP 2006

PB - Association for Computational Linguistics (ACL)

T2 - 11th Conference on Empirical Methods in Natural Language Proceessing, EMNLP 2006, Held in Conjunction with COLING/ACL 2006

Y2 - 22 July 2006 through 23 July 2006

ER -

Hockenmaier J, Joshi AK, Dill KA. Protein folding and chart parsing. In COLING/ACL 2006 - EMNLP 2006: 2006 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference. Association for Computational Linguistics (ACL). 2006. p. 293-300. (COLING/ACL 2006 - EMNLP 2006: 2006 Conference on Empirical Methods in Natural Language Processing, Proceedings of the Conference). doi: 10.3115/1610075.1610117

Protein folding and chart parsing

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