Its target predictions are generated by MirTarget, a bioinformatics tool developed using thousands of miRNA–target interactions identified through high-throughput sequencing experiments. The system applies machine-learning methods to features associated with miRNA binding and target downregulation.

The database provides predicted targets for human, mouse, rat, dog, and chicken, with search options based on miRNA names or gene targets. Researchers can also submit their own sequences for custom target prediction. To support functional studies, miRDB includes the FuncMir Collection, which presents functionally active miRNAs identified in humans and mice through computational analyses and literature mining, together with associated annotations.

Other resources include miRNA expression profiles for hundreds of cell lines, allowing users to focus searches on targets expressed in a selected cell line, and an interface for integrated analysis of target predictions and Gene Ontology data. miRDB also offers target mining, data downloads, statistics, and guidance for users.