Accessibility in proteins and RNAs interactions prediction with machine learning: are we overlooking non-experts?

Abstract

The increasing growth in the volume of biomolecular data has introduced significant challenges for extracting meaningful molecular-level insights, particularly in predicting interactions between biological sequences such as DNA, RNA, and proteins. These interactions are fundamental to complex biological processes, including gene regulation and immune response. Artificial Intelligence (AI) has played a major role in advancing discoveries in this field, enabling the identification of novel interactions, as demonstrated by various predictive modeling studies. Despite the growing number of scientific publications in this domain, accessibility to practical computational tools has not progressed at the same pace. Existing studies differ substantially in availability: some provide only methodological descriptions, others release source code exclusively for experimental reproducibility, and only a limited number deliver fully automated solutions ready for broad use. Given this context, this paper investigates state-of-the-art studies in biological sequence interaction prediction, emphasizing the public accessibility and usability of available tools, especially for researchers who are not experts in AI or computational methods. We compile and discuss the input requirements of current tools, along with the types of outputs they generate, enabling users to better understand the scenarios in which each solution can be effectively applied. Furthermore, we analyze accessibility-related aspects to support informed selection of tools according to user expertise, ranging from web-based servers with pretrained models that require minimal computational skills to fully end-to-end frameworks capable of training new models on user-defined datasets, though often lacking user-friendly interfaces.