An Isoform-Centric, Structure-Aware Framework for Protein Function Prediction and Evaluation, Instantiated in 3DisoDeepPF

Understanding and accurately predicting function across protein isoforms has been a long-standing challenge with profound implications for both biological and translational research. However, most functional annotations and benchmarks remain tied to genes or reference protein sequences, leaving limited support for distinguishing protein isoforms from the same gene whose sequence, structure and domain composition may lead to different functions. To address this gap, we developed an isoform-centric framework for protein function and domain annotation that integrates a dense graph of sequence and structure similarity with protein features. We implemented this framework as 3DisoDeepPF, a graph-based multimodal model, and applied it to a breast cancer isoform atlas. Across canonical benchmarks and evaluations at isoform resolution, 3DisoDeepPF showed strong performance in predicting GO terms and Pfam domains and remained robust in tests with homology control. It further captured changes in Pfam domain composition among isoforms from the same gene, including reference-relative domain gain and loss. An evidence tracing module links predicted labels to supporting proteins in the graph, as illustrated by the calcium and integrin binding protein 1 (CIB1). Together, this study provides a framework informed by protein structure for function and domain annotation at isoform resolution, converting human protein isoform diversity into traceable functional evidence for cancer atlas interpretation.