iPARTS

'iPARTS' is a web server that offers a novel approach to aligning two RNA 3D structures. The software tool employs a structural alphabet (SA)-based approach, which involves transforming RNA 3D structures into 1D sequences of SA letters. To achieve this, iPARTS first derives a Ramachandran-like diagram of RNAs by plotting nucleotides on a 2D axis using their two pseudo-torsion angles, eta, and theta. The affinity propagation clustering algorithm is applied to this plot to obtain an SA of 23-nt conformations.
The SA-encoded sequences of the two RNA 3D structures are then compared using classical sequence alignment methods to determine their structural similarities. iPARTS provides four output alignments: global, semi-global, local, and normalized local structural alignments. Global alignment is useful for determining overall structural similarity, while semi-global alignments can detect structural motifs or substructures. Local alignments are ideal for finding locally similar substructures, and normalized local structural alignments help identify more similar local substructures without non-similar internal fragments.
In addition, iPARTS offers a graphical display that enables users to visually view, rotate, and enlarge the superposition of aligned RNA 3D structures. This feature is particularly useful for analyzing the results of structural alignments.