• FP-Zernike is an open-source toolkit that computes Zernike descriptors from feature points, enabling fast and accurate protein structure retrieval on custom datasets.
• It outperforms existing methods in retrieval and binary classification accuracy across diverse benchmarks, while requiring only 4–9 seconds for retrieval on a database of 590,685 structures.
• The toolkit provides a simple command-line interface and supports local deployment, overcoming the limitations of web-based tools for large-scale structural database construction.
• FP-Zernike facilitates the construction of descriptor databases for the PDB and other datasets, offering a practical solution for efficient structure similarity analysis.