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Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods

BACKGROUND: Elucidation of protein-protein interaction (PPI) networks is important for understanding disease mechanisms and for drug discovery. Tertiary-structure-based in silico PPI prediction methods have been developed with two typical approaches: a method based on template matching with known pr...

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Autores principales: Ohue, Masahito, Matsuzaki, Yuri, Shimoda, Takehiro, Ishida, Takashi, Akiyama, Yutaka
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4044902/
https://www.ncbi.nlm.nih.gov/pubmed/24564962
http://dx.doi.org/10.1186/1753-6561-7-S7-S6
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author Ohue, Masahito
Matsuzaki, Yuri
Shimoda, Takehiro
Ishida, Takashi
Akiyama, Yutaka
author_facet Ohue, Masahito
Matsuzaki, Yuri
Shimoda, Takehiro
Ishida, Takashi
Akiyama, Yutaka
author_sort Ohue, Masahito
collection PubMed
description BACKGROUND: Elucidation of protein-protein interaction (PPI) networks is important for understanding disease mechanisms and for drug discovery. Tertiary-structure-based in silico PPI prediction methods have been developed with two typical approaches: a method based on template matching with known protein structures and a method based on de novo protein docking. However, the template-based method has a narrow applicable range because of its use of template information, and the de novo docking based method does not have good prediction performance. In addition, both of these in silico prediction methods have insufficient precision, and require validation of the predicted PPIs by biological experiments, leading to considerable expenditure; therefore, PPI prediction methods with greater precision are needed. RESULTS: We have proposed a new structure-based PPI prediction method by combining template-based prediction and de novo docking prediction. When we applied the method to the human apoptosis signaling pathway, we obtained a precision value of 0.333, which is higher than that achieved using conventional methods (0.231 for PRISM, a template-based method, and 0.145 for MEGADOCK, a non-template-based method), while maintaining an F-measure value (0.285) comparable to that obtained using conventional methods (0.296 for PRISM, and 0.220 for MEGADOCK). CONCLUSIONS: Our consensus method successfully predicted a PPI network with greater precision than conventional template/non-template methods, which may thus reduce the cost of validation by laboratory experiments for confirming novel PPIs from predicted PPIs. Therefore, our method may serve as an aid for promoting interactome analysis.
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spelling pubmed-40449022014-06-19 Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods Ohue, Masahito Matsuzaki, Yuri Shimoda, Takehiro Ishida, Takashi Akiyama, Yutaka BMC Proc Proceedings BACKGROUND: Elucidation of protein-protein interaction (PPI) networks is important for understanding disease mechanisms and for drug discovery. Tertiary-structure-based in silico PPI prediction methods have been developed with two typical approaches: a method based on template matching with known protein structures and a method based on de novo protein docking. However, the template-based method has a narrow applicable range because of its use of template information, and the de novo docking based method does not have good prediction performance. In addition, both of these in silico prediction methods have insufficient precision, and require validation of the predicted PPIs by biological experiments, leading to considerable expenditure; therefore, PPI prediction methods with greater precision are needed. RESULTS: We have proposed a new structure-based PPI prediction method by combining template-based prediction and de novo docking prediction. When we applied the method to the human apoptosis signaling pathway, we obtained a precision value of 0.333, which is higher than that achieved using conventional methods (0.231 for PRISM, a template-based method, and 0.145 for MEGADOCK, a non-template-based method), while maintaining an F-measure value (0.285) comparable to that obtained using conventional methods (0.296 for PRISM, and 0.220 for MEGADOCK). CONCLUSIONS: Our consensus method successfully predicted a PPI network with greater precision than conventional template/non-template methods, which may thus reduce the cost of validation by laboratory experiments for confirming novel PPIs from predicted PPIs. Therefore, our method may serve as an aid for promoting interactome analysis. BioMed Central 2013-12-20 /pmc/articles/PMC4044902/ /pubmed/24564962 http://dx.doi.org/10.1186/1753-6561-7-S7-S6 Text en Copyright © 2013 Ohue et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Proceedings
Ohue, Masahito
Matsuzaki, Yuri
Shimoda, Takehiro
Ishida, Takashi
Akiyama, Yutaka
Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods
title Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods
title_full Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods
title_fullStr Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods
title_full_unstemmed Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods
title_short Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods
title_sort highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4044902/
https://www.ncbi.nlm.nih.gov/pubmed/24564962
http://dx.doi.org/10.1186/1753-6561-7-S7-S6
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