ArticlePloS one2014
Protein-RNA complexes and efficient automatic docking: expanding RosettaDock possibilities.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Differentiation of RNA-protein docking structures through molecular dynamics simulation and machine learning methods.Briefings in bioinformatics · 2026Article
- Structural comparison of homologous protein-RNA interfaces reveals widespread overall conservation contrasted with versatility in polar contacts.PLoS computational biology · 2024Article
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
- Computational tools to study RNA-protein complexes.Frontiers in molecular biosciences · 2022Review
- Article
- Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins.PLoS computational biology · 2019Article
- Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking.Structure (London, England : 1993) · 2019Article
- PredPRBA: Prediction of Protein-RNA Binding Affinity Using Gradient Boosted Regression Trees.Frontiers in genetics · 2019Article
- Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes.RNA (New York, N.Y.) · 2018Article
- Review
- Structural insights into the stimulation of S. pombe Dnmt2 catalytic efficiency by the tRNA nucleoside queuosine.Scientific reports · 2018Article
- A pair-conformation-dependent scoring function for evaluating 3D RNA-protein complex structures.PloS one · 2017Article
- Template-Based Modeling of Protein-RNA Interactions.PLoS computational biology · 2016Article
- Protocols for Molecular Modeling with Rosetta3 and RosettaScripts.Biochemistry · 2016Review
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Authors and funding
4 authors.
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Abstract
Protein-RNA complexes provide a wide range of essential functions in the cell. Their atomic experimental structure solving, despite essential to the understanding of these functions, is often difficult and expensive. Docking approaches that have been developed for proteins are often challenging to adapt for RNA because of its inherent flexibility and the structural data available being relatively scarce. In this study we adapted the RosettaDock protocol for protein-RNA complexes both at the nucleotide and atomic levels. Using a genetic algorithm-based strategy, and a non-redundant protein-RNA dataset, we derived a RosettaDock scoring scheme able not only to discriminate but also score efficiently docking decoys. The approach proved to be both efficient and robust for generating and identifying suitable structures when applied to two protein-RNA docking benchmarks in both bound and unbound settings. It also compares well to existing strategies. This is the first approach that currently offers a multi-level optimized scoring approach integrated in a full docking suite, leading the way to adaptive fully flexible strategies.
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