Localization of a protein within a cell encompasses various processes and signaling events, including guidance of signal peptides. Accurate prediction of subcellular and suborganellar protein localization, as well as signal peptides, is crucial for understanding protein function and provides valuable insights into cellular mechanisms. Although many computational methods can predict either general protein localization, suborganellar localization, or signal peptides, the lack of comprehensive and intuitive interpretation, insufficient coverage of localization types, and issues related to ease of use are some common limitations. In this chapter, we introduce MULocDeep, an advanced web server designed for the prediction of protein localization at both subcellular and suborganellar levels, as well as the identification of signal peptides and their corresponding cleavage sites. This web server integrates a sophisticated protein large language model, enabling highly accurate predictions and facilitating the interpretation of results. The server also includes multiple interactive interfaces that enhance the clarity and accessibility of predictions, particularly concerning motif patterns within protein sequences. Furthermore, we demonstrate the practical functionality of the MULocDeep web server, providing detailed instructions on how to utilize the server and interpret the results for both localization and signal peptide prediction. The MULocDeep web server is publicly available at https://www.mu-loc.org/ .