ArticleNucleic acids research2006
Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed, 122 citations in OpenAlex.
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- Generation of RNA aptamers against chikungunya virus E2 envelope protein.Journal of virology · 2025Article
- RNA-protein interaction prediction without high-throughput data: An overview and benchmark ofComputational and structural biotechnology journal · 2024Article
- Advances and Challenges in Scoring Functions for RNA-Protein Complex Structure Prediction.Biomolecules · 2024Review
- Role of Optimization in RNA-Protein-Binding Prediction.Current issues in molecular biology · 2024Article
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- PRIP: A Protein-RNA Interface Predictor Based on Semantics of Sequences.Life (Basel, Switzerland) · 2022Article
- Computational tools to study RNA-protein complexes.Frontiers in molecular biosciences · 2022Review
- A Max-Margin Model for Predicting Residue-Base Contacts in Protein-RNA Interactions.Life (Basel, Switzerland) · 2021Article
- DeepDISE: DNA Binding Site Prediction Using a Deep Learning Method.International journal of molecular sciences · 2021Article
- 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 two-step probing method to compare lysine accessibility across macromolecular complex conformations.RNA biology · 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
- A structural dissection of protein-RNA interactions based on different RNA base areas of interfaces.RSC advances · 2018Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-RNA interactions play essential roles in a number of regulatory mechanisms for gene expression such as RNA splicing, transport, translation and post-transcriptional control. As the number of available protein-RNA complex 3D structures has increased, it is now possible to statistically examine protein-RNA interactions based on 3D structures. We performed computational analyses of 86 representative protein-RNA complexes retrieved from the Protein Data Bank. Interface residue propensity, a measure of the relative importance of different amino acid residues in the RNA interface, was calculated for each amino acid residue type (residue singlet interface propensity). In addition to the residue singlet propensity, we introduce a new residue-based propensity, which gives a measure of residue pairing preferences in the RNA interface of a protein (residue doublet interface propensity). The residue doublet interface propensity contains much more information than the sum of two singlet propensities alone. The prediction of the RNA interface using the two types of propensities plus a position-specific multiple sequence profile can achieve a specificity of about 80%. The prediction method was then applied to the 3D structure of two mRNA export factors, TAP (Mex67) and UAP56 (Sub2). The prediction enables us to point out candidate RNA interfaces, part of which are consistent with previous experimental studies and may contribute to elucidation of atomic mechanisms of mRNA export.
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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.