RNA tertiary structure modeling with BRiQ potential in CASP15
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Updated: Jul 17, 2025

RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
Ke Chen1,2, Yaoqi Zhou3, Sheng Wang4
1University of Science and Technology of China, Hefei, China.
Abstract:
We describe the modeling method for RNA tertiary structures employed by team AIchemy_RNA2 in the 15th Critical Assessment of Structure Prediction (CASP15). The method consists of the following steps. Firstly, secondary structure information was derived from various manually-verified sources. With this information, the full length RNA was fragmented into structural modules. The structures of each module were predicted and then assembled into the full structure. To reduce the searching conformational space, an RNA structure was organized into an optimal base folding tree. And to further improve the sampling efficiency, the energy surface was smoothed at high temperatures during the Monte Carlo sampling to make it easier to move across the energy barrier. The statistical potential energy function BRiQ was employed during Monte Carlo energy optimization.
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