High dimensional indexing for protein structure matching using bowties

Zi H. Huang; Xiaofang Zhou; Dawei Song

doi:10.1142/9781860947322_0003

High dimensional indexing for protein structure matching using bowties

Zi H. Huang^*, Xiaofang Zhou, Dawei Song

^*Corresponding author for this work

University of Queensland

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

6 Citations (Scopus)

Abstract

For determining functionality dependencies between two proteins, both represented as 3D structures, it is an essential condition that they have a matching structure. As 3D structures for proteins are large, complex and constantly evolving, it is very time-consuming to identify possible locations and sizes of such a matching structure for a given protein against a large protein database. In this paper, we introduce a novel representation model and apply a transformation and formalization to this problem. We then propose a database solution by using innovative high dimensional indexing mechanisms. Experimental results demonstrate a promising performance of the high dimensional indexing to this biologically critical but previously computationally prohibitive problem.

Original language	English
Title of host publication	Proceedings of the 3rd Asia-Pacific Bioinformatics Conference, APBC 2005
Publisher	Imperial College Press
Pages	21-30
Number of pages	10
ISBN (Print)	1860944779, 9781860944772
DOIs	https://doi.org/10.1142/9781860947322_0003
Publication status	Published - 2005
Externally published	Yes
Event	3rd Asia-Pacific Bioinformatics Conference, APBC 2005 - Singapore, Singapore Duration: 17 Jan 2005 → 21 Jan 2005

Publication series

Name	Series on Advances in Bioinformatics and Computational Biology
Volume	1
ISSN (Print)	1751-6404

Conference

Conference	3rd Asia-Pacific Bioinformatics Conference, APBC 2005
Country/Territory	Singapore
City	Singapore
Period	17/01/05 → 21/01/05

Access to Document

10.1142/9781860947322_0003

Cite this

@inproceedings{405ca36ef91e473aa9be66e097d68ab9,

title = "High dimensional indexing for protein structure matching using bowties",

abstract = "For determining functionality dependencies between two proteins, both represented as 3D structures, it is an essential condition that they have a matching structure. As 3D structures for proteins are large, complex and constantly evolving, it is very time-consuming to identify possible locations and sizes of such a matching structure for a given protein against a large protein database. In this paper, we introduce a novel representation model and apply a transformation and formalization to this problem. We then propose a database solution by using innovative high dimensional indexing mechanisms. Experimental results demonstrate a promising performance of the high dimensional indexing to this biologically critical but previously computationally prohibitive problem.",

author = "Huang, \{Zi H.\} and Xiaofang Zhou and Dawei Song",

year = "2005",

doi = "10.1142/9781860947322\_0003",

language = "English",

isbn = "1860944779",

series = "Series on Advances in Bioinformatics and Computational Biology",

publisher = "Imperial College Press",

pages = "21--30",

booktitle = "Proceedings of the 3rd Asia-Pacific Bioinformatics Conference, APBC 2005",

note = "3rd Asia-Pacific Bioinformatics Conference, APBC 2005 ; Conference date: 17-01-2005 Through 21-01-2005",

}

Huang, ZH, Zhou, X & Song, D 2005, High dimensional indexing for protein structure matching using bowties. in Proceedings of the 3rd Asia-Pacific Bioinformatics Conference, APBC 2005. Series on Advances in Bioinformatics and Computational Biology, vol. 1, Imperial College Press, pp. 21-30, 3rd Asia-Pacific Bioinformatics Conference, APBC 2005, Singapore, Singapore, 17/01/05. https://doi.org/10.1142/9781860947322_0003

High dimensional indexing for protein structure matching using bowties. / Huang, Zi H.; Zhou, Xiaofang; Song, Dawei.
Proceedings of the 3rd Asia-Pacific Bioinformatics Conference, APBC 2005. Imperial College Press, 2005. p. 21-30 (Series on Advances in Bioinformatics and Computational Biology; Vol. 1).

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

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AU - Huang, Zi H.

AU - Zhou, Xiaofang

AU - Song, Dawei

PY - 2005

Y1 - 2005

N2 - For determining functionality dependencies between two proteins, both represented as 3D structures, it is an essential condition that they have a matching structure. As 3D structures for proteins are large, complex and constantly evolving, it is very time-consuming to identify possible locations and sizes of such a matching structure for a given protein against a large protein database. In this paper, we introduce a novel representation model and apply a transformation and formalization to this problem. We then propose a database solution by using innovative high dimensional indexing mechanisms. Experimental results demonstrate a promising performance of the high dimensional indexing to this biologically critical but previously computationally prohibitive problem.

AB - For determining functionality dependencies between two proteins, both represented as 3D structures, it is an essential condition that they have a matching structure. As 3D structures for proteins are large, complex and constantly evolving, it is very time-consuming to identify possible locations and sizes of such a matching structure for a given protein against a large protein database. In this paper, we introduce a novel representation model and apply a transformation and formalization to this problem. We then propose a database solution by using innovative high dimensional indexing mechanisms. Experimental results demonstrate a promising performance of the high dimensional indexing to this biologically critical but previously computationally prohibitive problem.

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U2 - 10.1142/9781860947322_0003

DO - 10.1142/9781860947322_0003

M3 - Conference contribution

AN - SCOPUS:84863027373

SN - 1860944779

SN - 9781860944772

T3 - Series on Advances in Bioinformatics and Computational Biology

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BT - Proceedings of the 3rd Asia-Pacific Bioinformatics Conference, APBC 2005

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T2 - 3rd Asia-Pacific Bioinformatics Conference, APBC 2005

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ER -

High dimensional indexing for protein structure matching using bowties

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