RNA3DClust server

Segment RNA 3D structures using multiple clustering algorithms

Select PDB input

Enter PDB code (4 characters)

Upload PDB/mmCIF file (.pdb or .cif)

Chain: Single-atom representation:

Settings

Chain minimum length (nt)

Post-processing: segment lengths

Domain min. (nt)

Linker min. (nt)

Linker max. (nt)

Clustering Algorithm 1

Algorithm:

Apply post-processing

Reference segmentation (optional)

Provide reference partitions. Domains are separated by “;”. Discontinuous domain uses “+” to join segments. Unlisted residues become outliers.

Le Q.K., Angel E., Tahi F., Postic G. (2025).
Semi-supervised segmentation of RNA 3D structures using density-based clustering. Computational and Structural Biotechnology Journal, 27, 3966–3984

https://doi.org/10.1016/j.csbj.2025.08.037