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Title: Protein complex prediction via improved verification methods using constrained domain-domain matching.
Authors: Zhao, Yang
Hayashida, Morihiro  kyouindb  KAKEN_id
Nacher, Jose C
Nagamochi, Hiroshi  kyouindb  KAKEN_id
Akutsu, Tatsuya  kyouindb  KAKEN_id  orcid https://orcid.org/0000-0001-9763-797X (unconfirmed)
Author's alias: 阿久津, 達也
Keywords: protein complex prediction
integer programming
DDI
domain-domain interactions
PPI
protein-protein interactions
bioinformatics
protein complexes
constrained domain-domain matching
verification methods
Issue Date: Sep-2012
Publisher: Inderscience Enterprises
Journal title: International journal of bioinformatics research and applications
Volume: 8
Issue: 3-4
Start page: 210
End page: 227
Abstract: Identification of protein complexes within protein-protein interaction networks is one of the important objectives in functional genomics. Ozawa et al. proposed a verification method of protein complexes by introducing a structural constraint. In this paper, we propose an improved integer programming-based method based on the idea that a candidate complex should not be divided into many small complexes, and combination methods with maximal components and extreme sets. The results of computational experiments suggest that our methods outperform the method by Ozawa et al. We prove that the verification problems are NP-hard, which justifies the use of integer programming.
Rights: © 2012 Inderscience Enterprises Ltd.
This is not the published version. Please cite only the published version. この論文は出版社版でありません。引用の際には出版社版をご確認ご利用ください。
URI: http://hdl.handle.net/2433/172236
DOI(Published Version): 10.1504/IJBRA.2012.048970
PubMed ID: 22961452
Appears in Collections:Journal Articles

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