ArticleProceedings of the National Academy of Sciences of the United States of America2019
Protein-assisted RNA fragment docking (RnaX) for modeling RNA-protein interactions using ModelX.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 21 citations in OpenAlex.
- Opportunities for artificial intelligence and synthetic biology in designing living drug delivery systems.Advanced drug delivery reviews · 2026Review
- Artificial intelligence and first-principle methods in protein redesign: A marriage of convenience?Protein science : a publication of the Protein Society · 2025Article
- Overcoming translational barriers in RNA-protein docking: enhancing computational accuracy for targeted drug discovery.Future medicinal chemistry · 2025Review
- Identification of the Wnt signal peptide that directs secretion on extracellular vesicles.Science advances · 2024Article
- Synchronized motion of interface residues for evaluating protein-RNA complex binding affinity: Application to aptamer-mediated inhibition of TDP-43 aggregates.Protein science : a publication of the Protein Society · 2024Article
- HIPPO: HIstogram-based Pseudo-POtential for scoring protein-ssRNA fragment-based docking poses.BMC bioinformatics · 2024Article
- Bacterial expression of a designed single-chain IL-10 prevents severe lung inflammation.Molecular systems biology · 2023Article
- Predicting the mutation effects of protein-ligand interactions via end-point binding free energy calculations: strategies and analyses.Journal of cheminformatics · 2022Article
- Computational structure modeling for diverse categories of macromolecular interactions.Current opinion in structural biology · 2020Review
- ProteinFishing: a protein complex generator within the ModelX toolsuite.Bioinformatics (Oxford, England) · 2020Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA-protein interactions are crucial for such key biological processes as regulation of transcription, splicing, translation, and gene silencing, among many others. Knowing where an RNA molecule interacts with a target protein and/or engineering an RNA molecule to specifically bind to a protein could allow for rational interference with these cellular processes and the design of novel therapies. Here we present a robust RNA-protein fragment pair-based method, termed RnaX, to predict RNA-binding sites. This methodology, which is integrated into the ModelX tool suite (http://modelx.crg.es), takes advantage of the structural information present in all released RNA-protein complexes. This information is used to create an exhaustive database for docking and a statistical forcefield for fast discrimination of true backbone-compatible interactions. RnaX, together with the protein design forcefield FoldX, enables us to predict RNA-protein interfaces and, when sufficient crystallographic information is available, to reengineer the interface at the sequence-specificity level by mimicking those conformational changes that occur on protein and RNA mutagenesis. These results, obtained at just a fraction of the computational cost of methods that simulate conformational dynamics, open up perspectives for the engineering of RNA-protein interfaces.
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