ArticleNucleic acids research2011
Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed, 112 citations in OpenAlex.
- CAP: Commutative algebra prediction of protein-nucleic acid binding affinities.Machine learning: science and technology · 2025Article
- Single-sequence protein-RNA complex structure prediction by geometric attention-enabled pairing of biological language models.Cell systems · 2025Article
- Advances in Protein-RNA aptamer recognition and modeling: Current trends and future perspectives.Current opinion in structural biology · 2025Review
- Research on Plant RNA-Binding Protein Prediction Method Based on Improved Ensemble Learning.Biology · 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
- Advances and Challenges in Scoring Functions for RNA-Protein Complex Structure Prediction.Biomolecules · 2024Review
- Evaluating native-like structures of RNA-protein complexes through the deep learning method.Nature communications · 2023Article
- IDPsBind: a repository of binding sites for intrinsically disordered proteins complexes with known 3D structures.BMC molecular and cell biology · 2022Article
- PRIP: A Protein-RNA Interface Predictor Based on Semantics of Sequences.Life (Basel, Switzerland) · 2022Article
- Genetic information from discordant sibling pairs points to ESRP2 as a candidate trans-acting regulator of the CF modifier gene SCNN1B.Scientific reports · 2020Article
- PRIME-3D2D is a 3D2D model to predict binding sites of protein-RNA interaction.Communications biology · 2020Article
- How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms.Molecular cell · 2020Review
- Scoring Functions for Protein-RNA Complex Structure Prediction: Advances, Applications, and Future Directions.Communications in information and systems · 2020Article
- A structure-based model for the prediction of protein-RNA binding affinity.RNA (New York, N.Y.) · 2019Article
- circGSK3β promotes metastasis in esophageal squamous cell carcinoma by augmenting β-catenin signaling.Molecular cancer · 2019Article
- A deep learning framework to predict binding preference of RNA constituents on protein surface.Nature communications · 2019Article
- DLIGAND2: an improved knowledge-based energy function for protein-ligand interactions using the distance-scaled, finite, ideal-gas reference state.Journal of cheminformatics · 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
6 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
Abstract
Mechanistic understanding of many key cellular processes often involves identification of RNA binding proteins (RBPs) and RNA binding sites in two separate steps. Here, they are predicted simultaneously by structural alignment to known protein-RNA complex structures followed by binding assessment with a DFIRE-based statistical energy function. This method achieves 98% accuracy and 91% precision for predicting RBPs and 93% accuracy and 78% precision for predicting RNA-binding amino-acid residues for a large benchmark of 212 RNA binding and 6761 non-RNA binding domains (leave-one-out cross-validation). Additional tests revealed that the method makes no false positive prediction from 311 DNA binding domains but correctly detects six domains binding with both DNA and RNA. In addition, it correctly identified 31 of 75 unbound RNA-binding domains with 92% accuracy and 65% precision for predicted binding residues and achieved 86% success rate in its application to SCOP RNA binding domain superfamily (Structural Classification Of Proteins). It further predicts 25 targets as RBPs in 2076 structural genomics targets: 20 of 25 predicted ones (80%) are putatively RNA binding. The superior performance over existing methods indicates the importance of dividing structures into domains, using a Z-score to measure relative structural similarity, and a statistical energy function to measure protein-RNA binding affinity.
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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.