RNA tertiary structure modeling with BRiQ potential in CASP15
By K. Chen, Yaoqi Zhou, Sheng Wang, Peng Xiong. 2023
29 citations recorded by the source corpus.
We describe the modeling method for RNA tertiary structures employed by team AIchemy_RNA2 in the 15th Critical Assessment of Protein 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 motifs. The structures of each motif were predicted and then assembled into the full structure. To reduce the searching conformational space, a 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.
Subfields: Materials Chemistry, Molecular Biology, Computational Biology & Bioinformatics
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Citations in the corpus
- Accurate structure prediction of biomolecular interactions with AlphaFold 3 (2024, background): “We did not reach the performance of the best human-expert-aided CASP15 submission AIchemy_RNA2 39 (Fig.”
- Assessment of three-dimensional RNA structure prediction in CASP15 (2023, neutral): “In addition to not using deep learning, the top four RNA predictors shared the property that they were not servers and, based on their own accounts (see papers co-submitted for this CASP issue 65 – 68 ), they appeared to still make use of human intuition.”