MOTIVATION: Accurate in silico identification of B-cell epitope residues is crucial for antibody design and structure-guided vaccine development. Although recent protein language models and structure-aware methods can capture spatial information of tertiary structure when generating residue embeddings, most existing epitope predictors use these embeddings to perform classification for individual residues one by one, without enforcing spatial continuity for reported epitope residues. Such methods often result in biologically implausible predictions because B-cell epitope residues always cluster together on the antigen surface. RESULTS: We present RoBep, a region-oriented B-cell epitope predictor that explicitly models the spatial clustering of epitope residues. RoBep introduces a novel region constraint mechanism and combines the advanced protein language model ESM-Cambrian with an equivariant graph neural network. Our method outperforms existing structure-based methods on the benchmark dataset, demonstrating improvements of 26%, 45%, 13%, and 43% in F1, Matthews correlation coefficient, area under the precision-recall curve, and AUROC0.1, respectively. In addition to residue-level predictions, RoBep can also provide antibody-antigen binding regions. Importantly, the predicted epitope residues are ensured to be spatially compact, enhancing biological plausibility and practical relevance for immunotherapeutic design. AVAILABILITY AND IMPLEMENTATION: A user-friendly website for using RoBep is provided at https://huggingface.co/spaces/NielTT/RoBep. All datasets, source code used in this work, and implementation instructions of the website are publicly available at https://github.com/YitaoXU/RoBep.

MicroRNAs (miRNAs) are crucial regulators of gene expression at post-transcriptional level. Understanding origin and evolution of miRNAs will improve the current available algorithm for the prediction of novel miRNAs and their functions. Transposable elements (TEs) provide a natural mechanism for the origin of new miRNAs. In the paper, 2,583 miRNAs derived from TEs (MDTEs) were collected to construct a database named MDTE database (MDTE DB) for storing, searching, and analyzing MDTEs. The database provides a convenient source for studying the origin and evolution of miRNAs. Database URL:http://bioinf.njnu.edu.cn/MDTE/MDTE.php.