ArticleRNA biology
Highly accurate and high-resolution function prediction of RNA binding proteins by fold recognition and binding affinity prediction.
Article in RNA biology. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- ProRB: a structure-free unified framework for joint prediction and design of protein-RNA interactions.Nucleic acids research · 2026Article
- RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets.Nature communications · 2025Article
- RBProkCNN: Deep learning on appropriate contextual evolutionary information for RNA binding protein discovery in prokaryotes.Computational and structural biotechnology journal · 2024Article
- Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences.Briefings in bioinformatics · 2024Review
- Advances and Challenges in Scoring Functions for RNA-Protein Complex Structure Prediction.Biomolecules · 2024Review
- A comprehensive review of protein-centric predictors for biomolecular interactions: from proteins to nucleic acids and beyond.Briefings in bioinformatics · 2024Review
- Seq-RBPPred: Predicting RNA-Binding Proteins from Sequence.ACS omega · 2024Article
- Evaluating native-like structures of RNA-protein complexes through the deep learning method.Nature communications · 2023Article
- RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins.Briefings in bioinformatics · 2022Article
- Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Type.International journal of molecular sciences · 2020Review
- Scoring Functions for Protein-RNA Complex Structure Prediction: Advances, Applications, and Future Directions.Communications in information and systems · 2020Article
- Deep-RBPPred: Predicting RNA binding proteins in the proteome scale based on deep learning.Scientific reports · 2018Article
- Polymorphism in the serotonin transporter protein gene in Maltese dogs with degenerative mitral valve disease.Journal of veterinary science · 2018Article
- APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins.Nucleic acids research · 2017Article
- DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues.Nucleic acids research · 2017Article
- Review
- Advances in the characterization of RNA-binding proteins.Wiley interdisciplinary reviews. RNA · 2016Review
- THOC2 Mutations Implicate mRNA-Export Pathway in X-Linked Intellectual Disability.American journal of human genetics · 2015Article
- SNBRFinder: A Sequence-Based Hybrid Algorithm for Enhanced Prediction of Nucleic Acid-Binding Residues.PloS one · 2015Article
- Prediction and validation of the unexplored RNA-binding protein atlas of the human proteome.Proteins · 2014Article
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Authors and funding
3 authors.
Funding
Abstract
A full understanding of the mechanism of post- transcriptional regulation requires more than simple two- state prediction (binding or not binding) for RNA binding proteins. Here we report a sequence-based technique dedicated for predicting complex structures of protein and RNA by combining fold recognition with binding affinity prediction. The method not only provides a highly accurate complex structure prediction (77% of residues are within 4°A RMSD from native in average for the independent test set) but also achieves the best performing two-state binding or non-binding prediction with an accuracy of 98%, precision of 84%, and Mathews correlation coefficient (MCC) of 0.62. Moreover, it predicts binding residues with an accuracy of 84%, precision of 66% and MCC value of 0.51. In addition, it has a success rate of 77% in predicting RNA binding types (mRNA, tRNA or rRNA). We further demonstrate that it makes more than 10% improvement either in precision or sensitivity than PSI- BLAST, HHPRED and our previously developed structure- based technique. This method expects to be useful for highly accurate genome-scale, high-resolution prediction of RNA-binding proteins and their complex structures. A web server (SPOT) is freely available for academic users at http://sparks.informatics.iupui.edu.
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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.