Prediction of Intrinsically Disordered Regions That Bind RNA with DisoRDPbind.

Contributions of Folded and Disordered Domains to RNA Binding by HNRNPR.

RNA binding proteins (RBPs) interact with and tightly regulate the fate of messenger RNAs, but how RNA targets are recognized remains a challenging question. RBPs often contain multiple domains known to directly bind RNA, such as RNA recognition motifs (RRMs), as well as domains whose RNA binding capacity remains incom...

Experimental and Computational Approaches to Identify RNA–Protein Interactions

Comparisons of experimental techniques and computational prediction tools for RBP identification aim to facilitate more accurate mapping of RNA–protein interactomes, thereby advancing understanding of RBP functions and supporting the development of novel therapeutic interventions targeting RNA–protein complexes.

Bridging the gap between omics and structural data: A framework for interpreting protein-RNA interaction specificity

Protein-RNA interactions play a central role in many cellular processes, such as gene regulation, protein synthesis and viral infections. Although a few thousand protein-RNA complexes have been structurally characterized, they represent only a small fraction of all interactions. This lack of experimental data limits th...

DNAreader: accurate prediction of DNA-binding residues in structured and disordered proteins using transformers and contrastive learning

This work introduces DNAreader, the first predictor specifically designed to predict DBRs in the structured and disordered sequence regions, and develops the DNAreaderDBIDR module, which accurately predicts DNA-binding IDRs, providing flexibility to identify DBRs within IDRs or to predict entire disordered DNA-binding...

Interpretable prediction of nucleic acid-binding proteins using a protein language model

It is demonstrated that attention-based protein language models can accurately identify nucleic acid-binding proteins directly from sequence data and reveal biologically meaningful sequence determinants of binding, establishing an interpretable and scalable framework for proteome-wide characterization of protein–nuclei...

In silico designing of small molecules for targeting RNA: current landscape and future directions