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. 2014 Aug 11;42(15):9562–9572. doi: 10.1093/nar/gku707

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© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 2. — A flowchart of the KGSrna sampling algorithm. KGSrna takes as inputs an initial conformation and a file of hydrogen bonds A(N3)–U(H3) and G(H1)–C(N3) as distance constraints. Next, a pool of conformations is initialized with the input structure and then grown by repeatedly perturbing a randomly selected conformation from the pool with a rebuild or null-space perturbation at a 10/90 rate. If no clashes between atoms were introduced in the perturbed conformation, it is added to the pool. The procedure is repeated until a desired number n_struct of conformations is obtained.