ArticleBMC bioinformatics2011
Prediction of dinucleotide-specific RNA-binding sites in proteins.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 51 citations in OpenAlex.
- Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences.Briefings in bioinformatics · 2024Review
- Synonymous variants that disrupt messenger RNA structure are significantly constrained in the human population.GigaScience · 2021Article
- Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Type.International journal of molecular sciences · 2020Review
- RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines.Genes · 2020Article
- Graph Theory-Based Sequence Descriptors as Remote Homology Predictors.Biomolecules · 2019Article
- Partner-specific prediction of RNA-binding residues in proteins: A critical assessment.Proteins · 2019Article
- PredPRBA: Prediction of Protein-RNA Binding Affinity Using Gradient Boosted Regression Trees.Frontiers in genetics · 2019Article
- Individually double minimum-distance definition of protein-RNA binding residues and application to structure-based prediction.Journal of computer-aided molecular design · 2018Article
- Deciphering RNA-Recognition Patterns of Intrinsically Disordered Proteins.International journal of molecular sciences · 2018Article
- Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism.Nucleic acids research · 2018Article
- mRNA/protein sequence complementarity and its determinants: The impact of affinity scales.PLoS computational biology · 2017Article
- DRNApred, fast sequence-based method that accurately predicts and discriminates DNA- and RNA-binding residues.Nucleic acids research · 2017Article
- RPI-Bind: a structure-based method for accurate identification of RNA-protein binding sites.Scientific reports · 2017Article
- Systematic Analysis of the Binding Surfaces between tRNAs and Their Respective Aminoacyl tRNA Synthetase Based on Structural and Evolutionary Data.Frontiers in genetics · 2017Article
- A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs.PLoS computational biology · 2015Article
- Computational Prediction of RNA-Binding Proteins and Binding Sites.International journal of molecular sciences · 2015Review
- Quantifying sequence and structural features of protein-RNA interactions.Nucleic acids research · 2014Article
- Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures.BMC bioinformatics · 2014Article
- The dataset for protein-RNA binding affinity.Protein science : a publication of the Protein Society · 2013Article
- Evidence of direct complementary interactions between messenger RNAs and their cognate proteins.Nucleic acids research · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRegulation of gene expression, protein synthesis, replication and assembly of many viruses involve RNA-protein interactions. Although some successful computational tools have been reported to recognize RNA binding sites in proteins, the problem of specificity remains poorly investigated. After the nucleotide base composition, the dinucleotide is the smallest unit of RNA sequence information and many RNA-binding proteins simply bind to regions enriched in one dinucleotide. Interaction preferences of protein subsequences and dinucleotides can be inferred from protein-RNA complex structures, enabling a training-based prediction approach.
resultsWe analyzed basic statistics of amino acid-dinucleotide contacts in protein-RNA complexes and found their pairing preferences could be identified. Using a standard approach to represent protein subsequences by their evolutionary profile, we trained neural networks to predict multiclass target vectors corresponding to 16 possible contacting dinucleotide subsequences. In the cross-validation experiments, the accuracies of the optimum network, measured as areas under the curve (AUC) of the receiver operating characteristic (ROC) graphs, were in the range of 65-80%.
conclusionsDinucleotide-specific contact predictions have also been extended to the prediction of interacting protein and RNA fragment pairs, which shows the applicability of this method to predict targets of RNA-binding proteins. A web server predicting the 16-dimensional contact probability matrix directly from a user-defined protein sequence was implemented and made available at: http://tardis.nibio.go.jp/netasa/srcpred.
Indexed as
Identifiers
What OpenQuestion holds
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.