Pairwise protein structure alignment based on an orientation-independent representation of the backbone geometry

Jieping Ye; Ravi Janardan; Songtao Liu

Pairwise protein structure alignment based on an orientation-independent representation of the backbone geometry

Jieping Ye, Ravi Janardan, Songtao Liu

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

Abstract

Determining structural similarities between proteins is an important problem since it can help identify functional and evolutionary relationships. In this paper, an algorithm is proposed to align two protein structures. Given the protein backbones, the algorithm finds a rigid motion of one backbone onto the other such that large substructures are matched. The algorithm uses a representation of the backbones that is independent of their relative orientations in space and applies dynamic programming to this representation to compute an initial alignment, which is then refined iteratively. Experiments indicate that the algorithm is competitive with two well-known algorithms, namely DALI [12] and LOCK [19].

Original language	English (US)
Title of host publication	Proceedings of the International Conference on Tools with Artificial Intelligence
Pages	2-9
Number of pages	8
State	Published - 2003
Externally published	Yes
Event	Proceedings: 15th IEEE International Conference on Tools with artificial Intelligence - Sacramento, CA, United States Duration: Nov 3 2003 → Nov 5 2003

Other

Other	Proceedings: 15th IEEE International Conference on Tools with artificial Intelligence
Country/Territory	United States
City	Sacramento, CA
Period	11/3/03 → 11/5/03

Keywords

Dynamic programming
Frobenius norm
Rigid motion
Root-mean squared deviation
Singular value decomposition
Structure alignment

ASJC Scopus subject areas

Software

Cite this

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title = "Pairwise protein structure alignment based on an orientation-independent representation of the backbone geometry",

abstract = "Determining structural similarities between proteins is an important problem since it can help identify functional and evolutionary relationships. In this paper, an algorithm is proposed to align two protein structures. Given the protein backbones, the algorithm finds a rigid motion of one backbone onto the other such that large substructures are matched. The algorithm uses a representation of the backbones that is independent of their relative orientations in space and applies dynamic programming to this representation to compute an initial alignment, which is then refined iteratively. Experiments indicate that the algorithm is competitive with two well-known algorithms, namely DALI [12] and LOCK [19].",

keywords = "Dynamic programming, Frobenius norm, Rigid motion, Root-mean squared deviation, Singular value decomposition, Structure alignment",

author = "Jieping Ye and Ravi Janardan and Songtao Liu",

year = "2003",

language = "English (US)",

pages = "2--9",

booktitle = "Proceedings of the International Conference on Tools with Artificial Intelligence",

note = "Proceedings: 15th IEEE International Conference on Tools with artificial Intelligence ; Conference date: 03-11-2003 Through 05-11-2003",

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TY - GEN

T1 - Pairwise protein structure alignment based on an orientation-independent representation of the backbone geometry

AU - Ye, Jieping

AU - Janardan, Ravi

AU - Liu, Songtao

PY - 2003

Y1 - 2003

N2 - Determining structural similarities between proteins is an important problem since it can help identify functional and evolutionary relationships. In this paper, an algorithm is proposed to align two protein structures. Given the protein backbones, the algorithm finds a rigid motion of one backbone onto the other such that large substructures are matched. The algorithm uses a representation of the backbones that is independent of their relative orientations in space and applies dynamic programming to this representation to compute an initial alignment, which is then refined iteratively. Experiments indicate that the algorithm is competitive with two well-known algorithms, namely DALI [12] and LOCK [19].

AB - Determining structural similarities between proteins is an important problem since it can help identify functional and evolutionary relationships. In this paper, an algorithm is proposed to align two protein structures. Given the protein backbones, the algorithm finds a rigid motion of one backbone onto the other such that large substructures are matched. The algorithm uses a representation of the backbones that is independent of their relative orientations in space and applies dynamic programming to this representation to compute an initial alignment, which is then refined iteratively. Experiments indicate that the algorithm is competitive with two well-known algorithms, namely DALI [12] and LOCK [19].

KW - Dynamic programming

KW - Frobenius norm

KW - Rigid motion

KW - Root-mean squared deviation

KW - Singular value decomposition

KW - Structure alignment

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UR - http://www.scopus.com/inward/citedby.url?scp=0345529118&partnerID=8YFLogxK

M3 - Conference contribution

AN - SCOPUS:0345529118

SP - 2

EP - 9

BT - Proceedings of the International Conference on Tools with Artificial Intelligence

T2 - Proceedings: 15th IEEE International Conference on Tools with artificial Intelligence

Y2 - 3 November 2003 through 5 November 2003

ER -

Pairwise protein structure alignment based on an orientation-independent representation of the backbone geometry

Abstract

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Keywords

ASJC Scopus subject areas

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