RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites

Abstract RNA and protein interactions play crucial roles in multiple biological processes, while these interactions are significantly influenced by the structures and sequences of protein and RNA molecules. In this study, we first performed an analysis of RNA-protein interacting complexes, and ident...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Jiesi Luo, Liang Liu, Suresh Venkateswaran, Qianqian Song, Xiaobo Zhou
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2f4e8eb227b045399e1f4b448d66fc44
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:2f4e8eb227b045399e1f4b448d66fc44
record_format	dspace
spelling	oai:doaj.org-article:2f4e8eb227b045399e1f4b448d66fc442021-12-02T16:06:50ZRPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites10.1038/s41598-017-00795-42045-2322https://doaj.org/article/2f4e8eb227b045399e1f4b448d66fc442017-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-00795-4https://doaj.org/toc/2045-2322Abstract RNA and protein interactions play crucial roles in multiple biological processes, while these interactions are significantly influenced by the structures and sequences of protein and RNA molecules. In this study, we first performed an analysis of RNA-protein interacting complexes, and identified interface properties of sequences and structures, which reveal the diverse nature of the binding sites. With the observations, we built a three-step prediction model, namely RPI-Bind, for the identification of RNA-protein binding regions using the sequences and structures of both proteins and RNAs. The three steps include 1) the prediction of RNA binding regions on protein, 2) the prediction of protein binding regions on RNA, and 3) the prediction of interacting regions on both RNA and protein simultaneously, with the results from steps 1) and 2). Compared with existing methods, most of which employ only sequences, our model significantly improves the prediction accuracy at each of the three steps. Especially, our model outperforms the catRAPID by >20% at the 3rd step. All of these results indicate the importance of structures in RNA-protein interactions, and suggest that the RPI-Bind model is a powerful theoretical framework for studying RNA-protein interactions.Jiesi LuoLiang LiuSuresh VenkateswaranQianqian SongXiaobo ZhouNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-13 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jiesi Luo Liang Liu Suresh Venkateswaran Qianqian Song Xiaobo Zhou RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites
description	Abstract RNA and protein interactions play crucial roles in multiple biological processes, while these interactions are significantly influenced by the structures and sequences of protein and RNA molecules. In this study, we first performed an analysis of RNA-protein interacting complexes, and identified interface properties of sequences and structures, which reveal the diverse nature of the binding sites. With the observations, we built a three-step prediction model, namely RPI-Bind, for the identification of RNA-protein binding regions using the sequences and structures of both proteins and RNAs. The three steps include 1) the prediction of RNA binding regions on protein, 2) the prediction of protein binding regions on RNA, and 3) the prediction of interacting regions on both RNA and protein simultaneously, with the results from steps 1) and 2). Compared with existing methods, most of which employ only sequences, our model significantly improves the prediction accuracy at each of the three steps. Especially, our model outperforms the catRAPID by >20% at the 3rd step. All of these results indicate the importance of structures in RNA-protein interactions, and suggest that the RPI-Bind model is a powerful theoretical framework for studying RNA-protein interactions.
format	article
author	Jiesi Luo Liang Liu Suresh Venkateswaran Qianqian Song Xiaobo Zhou
author_facet	Jiesi Luo Liang Liu Suresh Venkateswaran Qianqian Song Xiaobo Zhou
author_sort	Jiesi Luo
title	RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites
title_short	RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites
title_full	RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites
title_fullStr	RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites
title_full_unstemmed	RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites
title_sort	rpi-bind: a structure-based method for accurate identification of rna-protein binding sites
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/2f4e8eb227b045399e1f4b448d66fc44
work_keys_str_mv	AT jiesiluo rpibindastructurebasedmethodforaccurateidentificationofrnaproteinbindingsites AT liangliu rpibindastructurebasedmethodforaccurateidentificationofrnaproteinbindingsites AT sureshvenkateswaran rpibindastructurebasedmethodforaccurateidentificationofrnaproteinbindingsites AT qianqiansong rpibindastructurebasedmethodforaccurateidentificationofrnaproteinbindingsites AT xiaobozhou rpibindastructurebasedmethodforaccurateidentificationofrnaproteinbindingsites
_version_	1718384833061715968

RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites

Ejemplares similares