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Computational methods for predicting hotspots at protein–RNA interfaces

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Abstract Protein–RNA interactions play essential roles in many critical biological events. A comprehensive understanding of the mechanisms underlying these interactions is helpful when studying cellular activities and therapeutic applications. Hotspots are a small portion of residues contributing much toward protein–RNA binding affinity. In pharmaceutical research, the hotspot residues are seen as the best option for designing small molecules to target proteins of therapeutic interest. With the accumulation of experimental data about protein–RNA interactions, computational methods have been produced for hotspot prediction on a large scale. In this review, we first present an overview of the existing databases for protein–RNA binding data. Furthermore, we outline the most adopted computational methods for hotspots prediction in protein–RNA interactions. Finally, we discuss the applications of hotspot prediction. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein‐RNA Recognition RNA Interactions with Proteins and Other Molecules > Protein‐RNA Interactions: Functional Implications RNA Methods > RNA Analyses In Vitro and In Silico
Prediction of hotspot residues within the interface of restrictocin and its substrate sarcin/ricin loop (SRL). (a) The crystal structure of restrictocin‐SRL complex (PDB ID: 1JBS). Restrictocin is shown as white cartoon and SRL as orange cartoon. The interfacial residues are highlighted with sphere style, and hotspot residues are colored in red, nonhotspot residues in blue. (b) Performance comparison of computational methods on the restrictocin‐SRL test set. Six parameters were evaluated including sensitivity (SEN), specificity (SPE), precision (PRE), accuracy (ACC), F1 score, and Matthew correlation coefficient (MCC)
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RNA Methods > RNA Analyses In Vitro and In Silico
RNA Interactions with Proteins and Other Molecules > Protein–RNA Interactions: Functional Implications
RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition

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