The 3D structure of RNA critically influences its functionality, and understanding this structure is vital for deciphering RNA biology. Experimental methods for determining RNA structures are labour-intensive, expensive, and time-consuming. Computational approaches have emerged as valuable tools, leveraging physics-based-principles and machine learning to predict RNA structures rapidly. Despite advancements, the accuracy of computational methods remains modest, especially when compared to protein structure prediction. Deep learning methods, while successful in protein structure prediction, have shown some promise for RNA structure prediction as well, but face unique challenges. This study systematically benchmarks state-of-the-art deep learning methods for RNA structure prediction across diverse datasets. Our aim is to identify factors influencing performance variation, such as RNA family diversity, sequence length, RNA type, multiple sequence alignment (MSA) quality, and deep learning model architecture. We show that generally ML-based methods perform much better than non-ML methods on most RNA targets, although the performance difference isn't substantial when working with unseen novel or synthetic RNAs. The quality of the MSA and secondary structure prediction both play an important role and most methods aren't able to predict non-Watson-Crick pairs in the RNAs. Overall among the automated 3D RNA structure prediction methods, DeepFoldRNA has the best prediction results followed by DRFold as the second best method. Finally, we also suggest possible mitigations to improve the quality of the prediction for future method development.

MOTIVATION: B-cell epitopes (BCEs) play a pivotal role in the development of peptide vaccines, immuno-diagnostic reagents and antibody production, and thus in infectious disease prevention and diagnostics in general. Experimental methods used to determine BCEs are costly and time-consuming. Therefore, it is essential to develop computational methods for the rapid identification of BCEs. Although several computational methods have been developed for this task, generalizability is still a major concern, where cross-testing of the classifiers trained and tested on different datasets has revealed accuracies of 51-53%. RESULTS: We describe a new method called EpitopeVec, which uses a combination of residue properties, modified antigenicity scales, and protein language model-based representations (protein vectors) as features of peptides for linear BCE predictions. Extensive benchmarking of EpitopeVec and other state-of-the-art methods for linear BCE prediction on several large and small datasets, as well as cross-testing, demonstrated an improvement in the performance of EpitopeVec over other methods in terms of accuracy and area under the curve. As the predictive performance depended on the species origin of the respective antigens (viral, bacterial and eukaryotic), we also trained our method on a large viral dataset to create a dedicated linear viral BCE predictor with improved cross-testing performance. AVAILABILITY AND IMPLEMENTATION: The software is available at https://github.com/hzi-bifo/epitope-prediction. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.