RNA FRABASE - RNA FRAgments search engine & dataBASE

Structural Elements

This menu allows a very fast screening of basic structural elements (residues, base pairs, multiplets, dinucleotide steps, stems, and single stranded regions of loops (apical, bulge, internal, and n-way junctions).
Select appropriate tab to find requested 3D structural elements.

Residue selection

Residue:

Parameters

Range

from

Sugar pucker pseudorotation phase angle (P):

Sugar pucker amplitude (Tm):

Glycosidic torsion angle (χ):

Exocyclic torsion angle around C4'-C5' (γ):

Other settings

Experimental method:

Include all models of the structure:

PDB's identifiers (optional)

Associated residues

Residue of the 1^st strand:

Residue of the 2^nd strand:

Base pairs classification

Leontis\Westhof's notation:

Saenger's notation:

Base-base parameters

Range

from

Shear (S_x):

Stretch (S_y):

Stagger (S_z):

Buckle (κ):

Propeller (ω):

Opening (σ):

Other settings

Experimental method:

Include all models of the structure:

PDB's identifiers (optional)

Associated residues

Residue of the 1^st strand:

Residue of the 2^nd strand:

Residue of the 3^rd strand:

Residue of the 4^th strand:

Residue of the 5^th strand:

Other settings

Experimental method:

Include all models of the structure:

PDB's identifiers (optional)

First base pair

Residue of the 1^st strand:

Residue of the 2^nd strand:

Second base pair

Residue of the 1^st strand:

Residue of the 2^nd strand:

Inter base pair parameters

Range

from

Shift (D_x):

Slide (D_y):

Rise (D_z):

Tilt (τ):

Roll (ρ):

Twist (Ω):

Other settings

Experimental method:

Include all models of the structure:

PDB's identifiers (optional)

Stem length

Undefined

Exact length Value:

Interval Minimum:

Maximum:

Sequence

First strand:

Second strand:

Other settings

Experimental method:

Include all models of the structure:

Case sensitive

PDB's identifiers (optional)

Sequence

Length	Sequence (optional)

Experimental method:

Include all models of the structure:

Case sensitive

Strand shift operation: