Nucleic acid 3D structure search and alignment with GTalign

Abstract

Structural comparison of nucleic acids, particularly RNA, is critical for understanding evolutionary and functional relationships beyond sequence similarity, yet efficient tools for large-scale 3D structure search and alignment remain scarce. We extend GTalign to support nucleic acid structures, enabling unified, high-performance alignment across macromolecules. Benchmarking on diverse nucleic acid datasets demonstrates improved alignment accuracy and substantially lower runtimes compared to existing methods. GTalign thus provides a scalable solution for nucleic acid structure comparison and database search. Availability and Implementation: https://github.com/minmarg/gtalign_alpha