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Cited by 37RNA and protein synthesis mechanismsProtein Structure and DynamicsRNA regulation and disease

RNA tertiary structure modeling with BRiQ potential in CASP15

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Chen, Ke, Zhou, Yaoqi, Wang, Sheng, Xiong, Peng·2023·Proteins: Structure, Function, and Bioinformatics
DOI 10.1002/prot.26574

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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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Cited by

Sorted by citations

Authors
Chen, K., Zhou, Y., Wang, S., & Xiong, P.
Affiliations
  • University of Science and Technology of China (CN)
  • Shenzhen Bay Laboratory (CN)
  • Shanghai Zelixir Biotech Co. Ltd Shanghai China
Corresponding author
  • Zhou, Yaoqi
  • Wang, Sheng
  • Xiong, Peng
ORCID
Venue
Proteins: Structure, Function, and Bioinformatics
Publisher
Wiley
Published
2023-08-28
Volume
91
Issue
12
Pages
1771-1778
ISSN
  • 0887-3585 (ISSN-L)
  • 1097-0134
DOI
10.1002/prot.26574
OpenAlex
W4386208722
Cited by
37
References
1
Citations by year
2026: 7 · 2025: 14 · 2024: 11 · 2023: 5
FWCI
3.29
Type
journal article
Language
en
Open access
Licence
onlinelibrary.wiley.com/termsAndConditions#vor (vor)
Locations
  • Proteins Structure Function and Bioinformatics (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • Griffith Research Online (submittedVersion, other-oa)
Funders
National Key Research and Development Program of China
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Keywords
RNA tertiary structure, CASP15, RNA structure prediction, secondary structure, structural modules, Monte Carlo sampling
MeSH terms
Algorithms, Monte Carlo Method, Protein Conformation, RNA

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