This deposit contains trained model weights for PLERIO, a sequence-based framework for imputing RNA–protein interactions from eCLIP data, as described in the IJMS manuscript: "Sequence-based models for RNA-Protein interactions imputation might be insufficient for novel signal prediction in eCLIP data." The preprint is available on bioRxiv. The included weights correspond to models trained on eCLIP datasets and are provided to support reproducibility and further benchmarking. These models rely solely on protein and RNA sequence features (e.g., ESM2 and UniRep embeddings) and do not incorporate structural or complex-aware information. `K562_singleprotein_weights.json` - logistic regression weights for K562 cell line single-protein models; `HepG2_singleprotein_weights.json` - logistic regression weights for HepG2 cell line single-protein models; `K562_multiprotein_weights.pt` - MLP weights for K562 cell line multi-protein model. Note: As discussed in the paper, PLERIO’s current multiprotein inference mode is prone to false positives/negatives and should not be used for de novo prediction on unseen proteins without caution. For usage instructions, preprocessing pipelines, and evaluation scripts, please refer to the associated GitHub repositories (PLERIO repository and supporting scripts).