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The previously indicated zipper stems were found in the consensus structures for both genes, thus suggesting evolutionary conservation of these structural elements.
Color-coded consensus structures for the individual sequences were displayed graphically using a program written in-house, and the outputs were combined into a composite image.
All consensus structures show compensatory mutations.
Colour plots of Consensus structures were generated using RNAalifold [ 50].
The Rfam sequence alignments come with consensus structures.
For evaluation purposes, we used the Rfam consensus structures as reference structures and compared them against the consensus structures predicted by the four tools.
Mountain plots can be produced with mountain.pl and cmount.pl from single and consensus structures, respectively.
Similar(4)
If all members of the protein family exhibit a geometric relationship between corresponding α-carbons then that relationship is preserved in the consensus structure.
For a pair-wise alignment against a consensus structure, output is as above except no consensus structure is produced.
We used fourteen active-conformation kinases (omitting Rio2) and generated a 52 residue consensus structure (consensus residues are listed in Supplementary Table S1).
80,000 models were generated and the lowest 5% (in full atom energy) were screened against the consensus structure.
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