CryoAlign2: efficient global and local Cryo-EM map retrieval based on parallel-accelerated local spatial structural features

Motivation: With the rapid advancements in Cryo-Electron Microscopy (Cryo-EM), an increasing number of high-resolution 3D density maps are being made publicly available, highlighting the urgent need for efficient structure similarity retrieval. Exploring map similarity at various levels is critical for fully utilizing these valuable resources. Our previously proposed CryoAlign can provide more accurate density map alignment while maintaining a low failure rate. However, CryoAlign only offers a method for aligning density maps, with low efficiency in local alignment, and has not yet been applied to the retrieval of Cryo-EM density maps. Results: We have developed an alignment-based retrieval tool to perform both global and local retrieval. Our approach adopts parallel-accelerated CryoAlign for high-precision 3D alignment and transforms density maps into point clouds for efficient retrieval and storage. Additionally, a multi-dimension scoring function is introduced to accurately assess structural similarities between superimposed density maps. To demonstrate its applicability, we conducted thorough testing across different retrieval tasks, such as global, local or hybrid similarity retrieval. Our tool achieves up to a 7-fold speedup while supporting precise local alignments. Comprehensive experiments demonstrate that even when one density map is entirely contained within another, our tool performs exceptionally well in high-resolution density map retrieval. It provides researchers with an efficient and accurate solution for density map similarity search. Availability and implementation: The source code, documentation, and sample data can be downloaded at http://github.com/JokerL2/CryoAlign2.