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Figure 6
Structural comparison of nucleic acids. Local comparative analysis of the P-site and E-site fMet-tRNA models from a 70S ribosome (PDB entry 3d5a chains Y and Z). The models are superposed and coloured according to the Flexible backbone score using a colour gradient (yellow implies similarity and red relative dissimilarity). The C1′, C4′, O3′ and O5′ atoms were used for the comparison in rough analogy with the four backbone atoms in proteins (any selection of atoms common to all nucleotides might have been selected). This allows straightforward visual identification of regions with low structural conservation (centre and left), whereas other regions (right) might visually appear dissimilar when superposed but are actually more conserved locally. This highlights how ProSMART can provide complementary information that cannot be readily achieved simply by looking at superposed structures or considering r.m.s.d. values.

Journal logoBIOLOGICAL
ISSN: 1399-0047
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