Protein-RNA interactions: structural characteristics and hotspot amino acids

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Structural information about protein-RNA complexes supports the understanding of crucial recognition processes in the cell, and it can allow the development of high affinity ligands to interfere with these processes. In this respect, the identification of amino acid hotspots is particularly important. In contrast to protein-protein interactions, in silico approaches for protein-RNA interactions lag behind in their development. Herein, we report an analysis of available protein-RNA structures. We assembled a data set of 322 crystal and NMR structures and analyzed them regarding interface properties. In addition, we describe a computational alanine-scanning approach which provides interaction scores for interface amino acids, allowing the identification of potential hotspots in protein-RNA interfaces. We have made the computational approach available as an online tool, which allows interaction scores to be calculated for any structure of a protein-RNA complex by uploading atomic coordinates to the PRI HotScore web server (

Original languageEnglish
Pages (from-to)1457-1465
Number of pages9
JournalRNA (New York, N.Y.)
Issue number11
Early online date9 Aug 2018
Publication statusPublished - Nov 2018


We are grateful for support from AstraZeneca, Bayer CropScience, Bayer HealthCare, Boehringer Ingelheim, Merck KGaA, and the Max-Planck-Society. The research was supported by the Deutsche Forschungsgemeinschaft (DFG; Emmy Noether program GR3592/2-1) and the European Reasearch Council (ERC; ERC starting grant, no. 678623).

FundersFunder number
Horizon 2020 Framework Programme
H2020 European Research Council678623
Deutsche ForschungsgemeinschaftGR3592/2-1


    • RNA-binding protein
    • alanine scanning
    • protein–RNA complex
    • ribonucleoprotein
    • secondary structure


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