ARTEMIS

ARTEMIS performs topology-independent superposition and structure-based sequence alignment of RNA 3D structures to enable comparative analysis of RNA folds and conserved motifs.

Key Features:

• Topology-Independent Superposition: Aligns RNA 3D structures without constraints from backbone topology, enabling comparison of sequence-permuted RNAs such as tRNA and Y RNA.
• Global RNA 3D Structure Alignment: Extends the ARTEM pairwise superposition method for RNA 3D modules to solve global alignment problems across entire RNA molecules.
• Performance in Benchmarks: In benchmark comparisons, outperforms existing state-of-the-art tools for both sequentially-ordered and topology-independent RNA 3D structure superposition tasks.
• Discovery of Conserved Motifs: Facilitates identification of conserved helical packing motifs across non-coding RNAs, including ribozymes and riboswitches, despite differing backbone topologies.

Scientific Applications:

• Comparative RNA Analysis: Enables detailed structural comparisons to reveal similarities and differences relevant to RNA function and evolution.
• Elucidation of RNA 3D Folds and Motifs: Allows exploration of RNA 3D fold space and motifs, including sequence-permuted arrangements inaccessible to topology-constrained methods.
• Functional Insights into Non-Coding RNAs: Supports analysis of spatial structures of non-coding RNAs to infer structure–function relationships, including studies of ribozymes and riboswitches.

Methodology:

Extends the ARTEM pairwise superposition approach to global alignment and implements topology-independent algorithms that enable unrestrained pairwise and global RNA 3D structure alignments beyond traditional heuristics.