ARTEM server: an online tool for nucleic acid 3D motif searches, 3D structure superposition and structure-based alignment

ARTEM Server is an online platform for comparative analysis of nucleic acid 3D structures, combining two complementary superposition methods based on the ARTEM algorithm. The server provides access to searches for local tertiary motifs using the ARTEM tool, which identifies local isosteric structural arrangements without relying on sequence, interaction annotations, or backbone connectivity. It also offers global structure alignment and search modes via ARTEMIS, a recent extension of ARTEM that performs global sequence alignments based on rigid-body structural superposition. ARTEMIS supports both classical sequentially ordered superpositions and alignments involving sequence permutations, and can enumerate alternative suboptimal matches, enabling structural searches within large molecules or across databases. Benchmarks reported in the original publications demonstrate that ARTEM and ARTEMIS outperform other tools and are particularly effective at detecting 3D motif and 3D fold similarities across diverse backbone contexts, including cases that are challenging for sequence-ordered or annotation-dependent methods. ARTEM Server unifies these capabilities in a web interface, accepting PDB/mmCIF inputs, supporting multiple query and reference structures, and providing interactive 3D visualization and exportable alignment and motif-matching data. ARTEM Server offers a user-friendly web-based environment for exploration of global nucleic acid folds and local tertiary motifs. The web server is available at https://artemserver.genesilico.pl/.