PocketMaster provides a flexible and automated tool for analyzing, clustering, and visualizing structural diversity in protein pockets.

PocketMaster is a flexible and automated tool for the analysis, clustering, and interpretation of protein pockets, enabling the exploration of structural diversity in functional and interacting regions of proteins. The tool provides multiple strategies for defining pocket alignment regions, along with various alignment algorithms and clustering approaches, allowing analyses to be customized for different research objectives. In addition, it automatically documents results and provides informative visualizations and reports. With these capabilities, PocketMaster can be particularly valuable in the early stages of drug design, where accurate analysis and selection of protein structures are essential. Using TYK2 as a case study, PocketMaster demonstrates its ability to identify conformational differences between kinase and pseudokinase domains, as well as subtypes of structures within each domain, reflecting the influence of various ligands and protein states. The estrogen receptor alpha (ERα) ligand-binding pocket was also analyzed as an additional case study, showing the tool's performance in capturing conformational variations in helix 12 (H12) between active (agonist-bound) and inactive (antagonist-bound) states. The results confirm known structural features and illustrate the potential of the tool for systematic exploration of protein pockets, quantitative assessment of differences, and support of rational drug design. The PocketMaster source code, together with example input files and documentation, can be accessed at https://github.com/narek-abelyan/PocketMaster .