ArticleMethods in molecular biology (Clifton, N.J.)2014
SPOT-Seq-RNA: predicting protein-RNA complex structure and RNA-binding function by fold recognition and binding affinity prediction.
Article in Methods in molecular biology (Clifton, N.J.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 49 citations in OpenAlex.
- RAPDOR: Using Jensen-Shannon Distance for the computational analysis of complex proteomics datasets.Nature communications · 2025Article
- DRBP-EDP: classification of DNA-binding proteins and RNA-binding proteins using ESM-2 and dual-path neural network.NAR genomics and bioinformatics · 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
- Projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles using scProjection.Nature communications · 2023Article
- RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins.Briefings in bioinformatics · 2022Article
- How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms.Molecular cell · 2020Review
- A structure-based model for the prediction of protein-RNA binding affinity.RNA (New York, N.Y.) · 2019Article
- TriPepSVM: de novo prediction of RNA-binding proteins based on short amino acid motifs.Nucleic acids research · 2019Article
- PredPRBA: Prediction of Protein-RNA Binding Affinity Using Gradient Boosted Regression Trees.Frontiers in genetics · 2019Article
- APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins.Nucleic acids research · 2017Article
- Sequence-Based Prediction of RNA-Binding Residues in Proteins.Methods in molecular biology (Clifton, N.J.) · 2017Article
- BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins.Nucleic acids research · 2016Article
- Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach.PLoS computational biology · 2016Article
- Computational Prediction of RNA-Binding Proteins and Binding Sites.International journal of molecular sciences · 2015Review
- Unzippers, resolvers and sensors: a structural and functional biochemistry tale of RNA helicases.International journal of molecular sciences · 2015Review
- Detecting protein-protein interactions with a novel matrix-based protein sequence representation and support vector machines.BioMed research international · 2015Article
- 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
4 authors at 3 institutions in 3 countries.
Funding
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. The online server and downloadable version of SPOT-Seq-RNA are available at http://sparks-lab.org/server/SPOT-Seq-RNA/.
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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.