ArticleNucleic acids research2016
Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 30 citations in OpenAlex.
- Revealing the Formation Mechanism of Key Metabolites During Japonica Rice Storage Driven by Microbial Functional Genes.Metabolites · 2026Article
- Predicting Single-Stranded DNA Oligonucleotides 3D Structures: An Open Issue.Computational and structural biotechnology journal · 2026Article
- HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses.BMC bioinformatics · 2024Article
- Low Molecular Weight Inhibitors Targeting the RNA-Binding Protein HuR.International journal of molecular sciences · 2023Article
- Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field.Nucleic acids research · 2022Article
- A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community).F1000Research · 2020Article
- 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
- Visualizing single-stranded nucleic acids in solution.Nucleic acids research · 2017Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-RNA complexes are important for many biological processes. However, structural modeling of such complexes is hampered by the high flexibility of RNA. Particularly challenging is the docking of single-stranded RNA (ssRNA). We have developed a fragment-based approach to model the structure of ssRNA bound to a protein, based on only the protein structure, the RNA sequence and conserved contacts. The conformational diversity of each RNA fragment is sampled by an exhaustive library of trinucleotides extracted from all known experimental protein-RNA complexes. The method was applied to ssRNA with up to 12 nucleotides which bind to dimers of the RNA recognition motifs (RRMs), a highly abundant eukaryotic RNA-binding domain. The fragment based docking allows a precise de novo atomic modeling of protein-bound ssRNA chains. On a benchmark of seven experimental ssRNA-RRM complexes, near-native models (with a mean heavy-atom deviation of <3 Å from experiment) were generated for six out of seven bound RNA chains, and even more precise models (deviation < 2 Å) were obtained for five out of seven cases, a significant improvement compared to the state of the art. The method is not restricted to RRMs but was also successfully applied to Pumilio RNA binding proteins.
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