RNAPOLIS

RNA FRABASE

RNA FRABASE:

wide range of structural data in a single repository
- RNA sequences and secondary structures (dot-bracket, graphics)
- atom coordinates, torsion and pseudotorsion angle values, sugar pucker parameters, base pair classification...)
an engine to search for RNA 3D fragments matching user-defined sequence / secondary structure pattern

Looking for experimentally determined RNA structures with particular sequence or secondary structure motif?

Visit RNA FRABASE to satisfy your scientific curiosity!

RNAComposer

Do you need to get a quick view of RNA 3D fold corresponding to your RNA sequence or secondary structure?

Explore RNAComposer for one-click prediction of RNA 3D structure!

RNAComposer is:

a fully automated knowledge-based system to predict three-dimensional structures of RNA
the fastest in its class and most user-friendly computational tool to be found internet-wide
publicly available and freely accessible webserver
and many more ...

RNApdbee

RNApdbee:

derives RNA secondary structure from atom coordinates (pdb files)
annotates canonical and non-canonical base pairs
supports knotted and unknotted structures
classifies pseudoknots according to their order
visualizes secondary structures
allows to compare all base pair identification methods

RNAlyzer

RNAlyzer is a computational method:

to compare RNA 3D models with the reference structure
to discriminate between correct and incorrect 3D models.

Unique fitures of RNAlyzer:

the idea based on local neighborhood, defined as a set of atoms included in the sphere, centered around user-defined atom,
simultaneous visualization of the distance between model and reference structure, at different accuracy levels (from individual residues to entire molecules).

RNAssess

RNAssess - a server that supports quality assessment through delivering both static and interactive visualizations, allowing an easy identification of native–like models and/or chosen structural regions of the analyzed molecule. It is available online and allows to apply all well–established measures used for RNA quality evaluation. A combination of results provided by RNAssess allows us to rank analyzed models.

RNAfitme

RNAfitme is a tool for:

remodels nucleobase- and nucleoside residue conformations in the fixed-backbone RNA 3D structure
reconstructs full-atom model of RNA from its backbone
refines RNA 3D model by reducing steric clashes

RNAvista

If you are exploring non-canonical interactions in RNA secondary structures try RNAvista. RNAvista allows predicting an extended RNA secondary structure from sequence or from the list of canonical base pairs. It is:

fully automated
publicly available
freely accessible webserver.