dc.contributor.author | Yang, Yuedong | |
dc.contributor.author | Zhao, Huiying | |
dc.contributor.author | Wang, Jihua | |
dc.contributor.author | Zhou, Yaoqi | |
dc.contributor.editor | Kihara, D | |
dc.date.accessioned | 2019-04-03T23:34:43Z | |
dc.date.available | 2019-04-03T23:34:43Z | |
dc.date.issued | 2014 | |
dc.identifier.isbn | 978-1-4939-0365-8 | |
dc.identifier.doi | 10.1007/978-1-4939-0366-5_9 | |
dc.identifier.uri | http://hdl.handle.net/10072/66241 | |
dc.description.abstract | RNA-binding proteins (RBPs) play key roles in RNA metabolism and post-transcriptional regulation. Computational methods have been developed separately for prediction of RBPs and RNA-binding residues by machine-learning techniques and prediction of protein-RNA complex structures by rigid or semiflexible structure-to-structure docking. Here, we describe a template-based technique called SPOT-Seq-RNA that integrates prediction of RBPs, RNA-binding residues, and protein-RNA complex structures into a single package. This integration is achieved by combining template-based structure-prediction software, SPARKS X, with binding affinity prediction software, DRNA. This tool yields reasonable sensitivity (46 %) and high precision (84 %) for an independent test set of 215 RBPs and 5,766 non-RBPs. SPOT-Seq-RNA is computationally efficient for genome-scale prediction of RBPs and protein-RNA complex structures. Its application to human genome study has revealed a similar sensitivity and ability to uncover hundreds of novel RBPs beyond simple homology. | |
dc.description.peerreviewed | Yes | |
dc.description.publicationstatus | Yes | |
dc.language | English | |
dc.language.iso | eng | |
dc.publisher | Springer | |
dc.publisher.place | United States | |
dc.relation.ispartofbooktitle | Protein Structure Prediction | |
dc.relation.ispartofchapter | 9 | |
dc.relation.ispartofstudentpublication | N | |
dc.relation.ispartofpagefrom | 119 | |
dc.relation.ispartofpageto | 130 | |
dc.relation.ispartofedition | 3rd | |
dc.relation.ispartofseries | Methods in Molecular Biology | |
dc.rights.retention | Y | |
dc.subject.fieldofresearch | Other chemical sciences | |
dc.subject.fieldofresearch | Biochemistry and cell biology | |
dc.subject.fieldofresearch | Other biological sciences not elsewhere classified | |
dc.subject.fieldofresearchcode | 3499 | |
dc.subject.fieldofresearchcode | 3101 | |
dc.subject.fieldofresearchcode | 319999 | |
dc.title | SPOT-Seq-RNA: Predicting Protein–RNA Complex Structure and RNA-Binding Function by Fold Recognition and Binding Affinity Prediction | |
dc.type | Book chapter | |
dc.type.description | B1 - Chapters | |
dc.type.code | B - Book Chapters | |
dc.description.version | Accepted Manuscript (AM) | |
gro.faculty | Office of the Snr Dep Vice Chancellor, Institute for Glycomics | |
gro.rights.copyright | © 2014 Springer. This is the author-manuscript version of this paper. It is reproduced here in accordance with the copyright policy of the publisher. Please refer to the publisher’s website for further information. | |
gro.hasfulltext | Full Text | |
gro.griffith.author | Zhou, Yaoqi | |
gro.griffith.author | Yang, Yuedong | |