We denote the nearest neighbour ion separations as r (r′)for B3 (B1) structures.
Most of the remaining structures with at most 1000 chords have much lower genus (computed for all base pairs): for 229 structures the genus is simply \(g=0\), for 225 structures it is lower than 50.
Probabilistic atlases for 37 structures are provided, along with average atlases.
MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes.
Fig. 11 Distribution of strain energies for 416 structures from the PDB.
The nearest neighbor ion separations for B1 (B2) structures are being r (r′), respectively.
For 2D structures, the distortion matrix can be rotated to reflect the changes in E along and across strike.
SCOP annotations could be retrieved for 238 structures (81.22%), Pfam annotations were available for 278 structures (94.88%) and GO annotations were available for 196 structures (66.89%).
RNA FRABASE was searched for 3D structures with an adenine bulge flanked by canonical base pairs as for A26.
However, to the best of our knowledge, elaborate energy parameters for G4 structures have not been available so far.
Using a window-size of 5 centered on each residue, we applied Lasso to identify the most variable regions for 1a3s (11 structures; Figure 6A).
