Exploiting Geometrical Properties on Protein Similarity Search

Saiful Akbar; Roland Wagner; Josef Küng

Exploiting Geometrical Properties on Protein Similarity Search

Institute for Application-oriented Knowledge Processing

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

Abstract

This paper discusses about several combinations of protein similarity measurement-methods, with respect to normalization, spatial partitions, geometrical properties, and distance metrics. We compare the effectiveness of possible combinations to each other. Our experiment shows that the feature based on fractional occupancy outperforms other methods. In addition, merging individual features might also yield good result. A prototype of 3D protein geometrical-similarity retrieval system is built for implementing our approach.

Original language	English
Title of host publication	Seventeenth International Workshop on Database and Expert Systems Applications (DEXA 2006)
Place of Publication	10662 Los Vaqueros Circle P.O. Box 3064, Los Alamitos, CA 90720-1314
Publisher	IEEE Computer Society
Pages	228-234
Number of pages	7
ISBN (Print)	0769526411, 9780769526416
Publication status	Published - Sept 2006

Publication series

Name	Proceedings - International Workshop on Database and Expert Systems Applications, DEXA
ISSN (Print)	1529-4188

Fields of science

102001 Artificial intelligence
102006 Computer supported cooperative work (CSCW)
102010 Database systems
102014 Information design
102015 Information systems
102016 IT security
102028 Knowledge engineering
102019 Machine learning
102022 Software development
102025 Distributed systems
502007 E-commerce
505002 Data protection
506002 E-government
509018 Knowledge management
202007 Computer integrated manufacturing (CIM)
102033 Data mining
102035 Data science

Cite this

Akbar, Saiful ; Wagner, Roland ; Küng, Josef. / Exploiting Geometrical Properties on Protein Similarity Search. Seventeenth International Workshop on Database and Expert Systems Applications (DEXA 2006). 10662 Los Vaqueros Circle P.O. Box 3064, Los Alamitos, CA 90720-1314 : IEEE Computer Society, 2006. pp. 228-234 (Proceedings - International Workshop on Database and Expert Systems Applications, DEXA).

@inproceedings{ecfe1a584b1f498eba203b928eab92e0,

title = "Exploiting Geometrical Properties on Protein Similarity Search",

abstract = "This paper discusses about several combinations of protein similarity measurement-methods, with respect to normalization, spatial partitions, geometrical properties, and distance metrics. We compare the effectiveness of possible combinations to each other. Our experiment shows that the feature based on fractional occupancy outperforms other methods. In addition, merging individual features might also yield good result. A prototype of 3D protein geometrical-similarity retrieval system is built for implementing our approach.",

author = "Saiful Akbar and Roland Wagner and Josef K{\"u}ng",

year = "2006",

month = sep,

language = "English",

isbn = "0769526411",

series = "Proceedings - International Workshop on Database and Expert Systems Applications, DEXA",

publisher = "IEEE Computer Society",

pages = "228--234",

booktitle = "Seventeenth International Workshop on Database and Expert Systems Applications (DEXA 2006)",

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Akbar, S, Wagner, R & Küng, J 2006, Exploiting Geometrical Properties on Protein Similarity Search. in Seventeenth International Workshop on Database and Expert Systems Applications (DEXA 2006)., 1698340, Proceedings - International Workshop on Database and Expert Systems Applications, DEXA, IEEE Computer Society, 10662 Los Vaqueros Circle P.O. Box 3064, Los Alamitos, CA 90720-1314, pp. 228-234.

Exploiting Geometrical Properties on Protein Similarity Search. / Akbar, Saiful; Wagner, Roland ; Küng, Josef.
Seventeenth International Workshop on Database and Expert Systems Applications (DEXA 2006). 10662 Los Vaqueros Circle P.O. Box 3064, Los Alamitos, CA 90720-1314: IEEE Computer Society, 2006. p. 228-234 1698340 (Proceedings - International Workshop on Database and Expert Systems Applications, DEXA).

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

TY - GEN

T1 - Exploiting Geometrical Properties on Protein Similarity Search

AU - Akbar, Saiful

AU - Wagner, Roland

AU - Küng, Josef

PY - 2006/9

Y1 - 2006/9

N2 - This paper discusses about several combinations of protein similarity measurement-methods, with respect to normalization, spatial partitions, geometrical properties, and distance metrics. We compare the effectiveness of possible combinations to each other. Our experiment shows that the feature based on fractional occupancy outperforms other methods. In addition, merging individual features might also yield good result. A prototype of 3D protein geometrical-similarity retrieval system is built for implementing our approach.

AB - This paper discusses about several combinations of protein similarity measurement-methods, with respect to normalization, spatial partitions, geometrical properties, and distance metrics. We compare the effectiveness of possible combinations to each other. Our experiment shows that the feature based on fractional occupancy outperforms other methods. In addition, merging individual features might also yield good result. A prototype of 3D protein geometrical-similarity retrieval system is built for implementing our approach.

UR - https://www.scopus.com/pages/publications/38049035303

M3 - Conference proceedings

SN - 0769526411

SN - 9780769526416

T3 - Proceedings - International Workshop on Database and Expert Systems Applications, DEXA

SP - 228

EP - 234

BT - Seventeenth International Workshop on Database and Expert Systems Applications (DEXA 2006)

PB - IEEE Computer Society

CY - 10662 Los Vaqueros Circle P.O. Box 3064, Los Alamitos, CA 90720-1314

ER -

Akbar S, Wagner R , Küng J. Exploiting Geometrical Properties on Protein Similarity Search. In Seventeenth International Workshop on Database and Expert Systems Applications (DEXA 2006). 10662 Los Vaqueros Circle P.O. Box 3064, Los Alamitos, CA 90720-1314: IEEE Computer Society. 2006. p. 228-234. 1698340. (Proceedings - International Workshop on Database and Expert Systems Applications, DEXA).

Exploiting Geometrical Properties on Protein Similarity Search

Abstract

Publication series

Fields of science

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Cite this