MEG-mod: A Multiview Enhanced Graph Neural Network for Knockdown Efficiency Prediction of Chemically Modified siRNA

Chemical modification is essential for improving the stability and knockdown efficiency of siRNAs. However, the combinatorial complexity of modification types and positions makes rational design difficult. Here, we propose MEG-mod, a deep learning framework for predicting the knockdown efficiency of chemically modified siRNAs. By integrating a literature-reading agent, manual curation, and public database resources, we construct an expanded data set. MEG-mod jointly models sequence context, physicochemical properties, chemical modification features, and duplex structural relationships. A structure-aware Transformer-based graph neural network captures base-pairing and adjacency dependencies within double-stranded siRNAs, while a modification-base fusion module models context-dependent modification effects. MEG-mod outperforms existing methods, achieving a pearson correlation coefficient of 0.9171. The attention mechanism enables interpretable analysis of key modification positions and modification types, and provides recommendations consistent with reported experimental designs. MEG-mod is available as a public web server (https://lmmd.ecust.edu.cn/megmod/), providing a practical tool for prediction and candidate prioritization of chemically modified siRNAs.