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Magnesium ions (Mg2+) are essential for the folding, functional expression, and structural stability of RNA molecules. However, predicting Mg2+–binding sites in RNA molecules based solely on RNA structures is still challenging. The molecular surface, characterized by a continuous shape with geometric and chemical properties, is important for RNA modelling and carries essential information for understanding the interactions between RNAs and Mg2+ ions. Here, we propose an approach named RNA–magnesium ion surface interaction fingerprinting (RMSIF), a geometric deep learning-based conceptual framework to predict magnesium ion binding sites in RNA structures. To evaluate the performance of RMSIF, we systematically enumerated decoy Mg2+ ions across a full-space grid within the range of 2 to 10 Å from the RNA molecule and made predictions accordingly. Visualization techniques were used to validate the prediction results and calculate success rates. Comparative assessments against state-of-the-art methods like MetalionRNA, MgNet, and Metal3DRNA revealed that RMSIF achieved superior success rates and accuracy in predicting Mg2+-binding sites. Additionally, in terms of the spatial distribution of Mg2+ ions within the RNA structures, a majority were situated in the deep grooves, while a minority occupied the shallow grooves. Collectively, the conceptual framework developed in this study holds promise for advancing insights into drug design, RNA co-transcriptional folding, and structure prediction. [ABSTRACT FROM AUTHOR]

Background: Due to the high cost of data collection for magnetization detection of media, the sample size is limited, it is not suitable to use deep learning method to predict its change trend. The prediction of physical and chemical properties of magnetized water and fertilizer (PCPMWF) by meta-learning can help to explore the effects of magnetized water and fertilizer irrigation on crops. Method: In this article, we propose a meta-learning optimization model based on the meta-learner LSTM in the field of regression prediction of PCPMWF. In meta-learning, LSTM is used to replace MAML's gradient descent optimizer for regression tasks, enables the meta-learner to learn the update rules of the LSTM, and apply it to update the parameters of the model. The proposed method is compared with the experimental results of MAML and LSTM to verify the feasibility and correctness. Results: The average absolute percentage error of the meta-learning optimization model of meta-learner LSTM is reduced by 0.37% compared with the MAML model, and by 4.16% compared with the LSTM model. The loss value of the meta-learning optimization model in the iterative process drops the fastest and steadily compared to the MAML model and the LSTM model. In cross-domain experiments, the average accuracy of the meta-learning optimized model can still reach 0.833. Conclusions: In the case of few sample, the proposed model is superior to the traditional LSTM model and the basic MAML model. And in the training of cross-domain datasets, this model performs best. [ABSTRACT FROM AUTHOR]