In computational structural biology, predicting metal-binding sites and their corresponding metal types is challenging due to the complexity of protein structures and interactions. Conventional sequence- and structure-based prediction approaches cannot capture the complex evolutionary relationships driving these interactions to facilitate understanding, while recent co-evolution-based approaches do not fully consider the entire structure of the co-evolved residue network. In this paper, we introduce MBGNN (Metal-Binding Graph Neural Network) that utilizes the entire co-evolved residue network and effectively captures the complex dependencies within protein structures via graph neural networks to enhance the prediction of co-evolved metal-binding residues and their associated metal types. Experimental results on a public dataset show that MBGNN outperforms existing co-evolution-based metal-binding prediction methods, and it is also competitive against recent sequence-based methods, showing the potential of integrating co-evolutionary insights with advanced machine learning to deepen our understanding of protein-metal interactions. The MBGNN code is publicly available at https://github.com/SRastegari/MBGNN.

Current deep learning models for classification tasks in computer vision are trained using mini-batches. In the present article, we take advantage of the relationships between samples in a mini-batch, using graph neural networks to aggregate information from similar images. This helps mitigate the adverse effects of alterations to the input images on classification performance. Diverse experiments on image-based object and scene classification show that this approach not only improves a classifier's performance but also increases its robustness to image perturbations and adversarial attacks. Further, we also show that mini-batch graph neural networks can help to alleviate the problem of mode collapse in Generative Adversarial Networks.