ArticleProteins2014
Prediction and validation of the unexplored RNA-binding protein atlas of the human proteome.
Article in Proteins, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed, 25 citations in OpenAlex.
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- Large-scale map of RNA-binding protein interactomes across the mRNA life cycle.Molecular cell · 2024Article
- HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence.Molecular cell · 2023Article
- Large-scale map of RNA binding protein interactomes across the mRNA life-cycle.bioRxiv : the preprint server for biology · 2023Article
- Scoring Functions for Protein-RNA Complex Structure Prediction: Advances, Applications, and Future Directions.Communications in information and systems · 2020Article
- Review
- Spectral and Hydrodynamic Analysis of West Nile Virus RNA-Protein Interactions by Multiwavelength Sedimentation Velocity in the Analytical Ultracentrifuge.Analytical chemistry · 2017Article
- Structural signatures of thermal adaptation of bacterial ribosomal RNA, transfer RNA, and messenger RNA.PloS one · 2017Article
- Sequence-Based Prediction of RNA-Binding Residues in Proteins.Methods in molecular biology (Clifton, N.J.) · 2017Article
- HOMCOS: an updated server to search and model complex 3D structures.Journal of structural and functional genomics · 2016Article
- Protein-RNA interactions: structural biology and computational modeling techniques.Biophysical reviews · 2016Review
- Advances in the characterization of RNA-binding proteins.Wiley interdisciplinary reviews. RNA · 2016Review
- BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins.Nucleic acids research · 2016Article
- Template-based prediction of protein function.Current opinion in structural biology · 2015Review
- Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.PloS one · 2014Article
- Prediction of RNA- and DNA-Binding Proteins Using Various Machine Learning Classifiers.Avicenna journal of medical biotechnologyArticle
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Detecting protein-RNA interactions is challenging both experimentally and computationally because RNAs are large in number, diverse in cellular location and function, and flexible in structure. As a result, many RNA-binding proteins (RBPs) remain to be identified. Here, a template-based, function-prediction technique SPOT-Seq for RBPs is applied to human proteome and its result is validated by a recent proteomic experimental discovery of 860 mRNA-binding proteins (mRBPs). The coverage (or sensitivity) is 42.6% for 1217 known RBPs annotated in the Gene Ontology and 43.6% for 860 newly discovered human mRBPs. Consistent sensitivity indicates the robust performance of SPOT-Seq for predicting RBPs. More importantly, SPOT-Seq detects 2418 novel RBPs in human proteome, 291 of which were validated by the newly discovered mRBP set. Among 291 validated novel RBPs, 61 are not homologous to any known RBPs. Successful validation of predicted novel RBPs permits us to further analysis of their phenotypic roles in disease pathways. The dataset of 2418 predicted novel RBPs along with confidence levels and complex structures is available at http://sparks-lab.org (in publications) for experimental confirmations and hypothesis generation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.