The RNA-Puzzles Assessments of RNA-Only Targets in CASP16.

IF 2.8 4区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Proteins-Structure Function and Bioinformatics Pub Date : 2025-10-03 DOI:10.1002/prot.70052

Eric Westhof, Hao Sun, Fan Bu, Zhichao Miao

引用次数: 0

Abstract

RNA-Puzzles was launched in 2011 as a collaborative effort dedicated to advancing and improving RNA 3D structure prediction. The automatic evaluation protocols for comparisons between prediction and experiment developed within RNA-Puzzles are applied to the 2024 CASP16 competition. The scores evaluate stereochemical parameters, Watson-Crick pairs, non-Watson-Crick pairs, and base stacking in addition to standard global parameters such as RMSD, TM-score, GDT, or lDDT. Several targets were particularly difficult owing to their size or multimerization. As noted in previous evaluations, although predictions that perform well on secondary structure may also achieve acceptable overall folds, they are insufficient to guarantee chemical precision or to correctly identify residues involved in non-Watson-Crick interactions. Both are essential for obtaining a valid three-dimensional architecture and for understanding the biological function of RNAs.

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CASP16中仅rna靶点的rna谜题评估。

RNA- puzzles于2011年推出，是一项致力于推进和改进RNA 3D结构预测的合作努力。在RNA-Puzzles中开发的预测和实验比较自动评估协议应用于2024 CASP16竞赛。除了RMSD、TM-score、GDT或lDDT等标准全局参数外，这些分数还评估立体化学参数、沃森-克里克对、非沃森-克里克对和碱基堆叠。有几个目标由于其大小或多用途而特别困难。正如在以前的评价中所指出的，虽然二级结构上表现良好的预测也可能获得可接受的整体褶皱，但它们不足以保证化学精度或正确识别非沃森-克里克相互作用中涉及的残基。两者对于获得有效的三维结构和理解rna的生物学功能都是必不可少的。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Proteins-Structure Function and Bioinformatics 生物-生化与分子生物学

CiteScore

5.90

自引率

3.40%

发文量

172

审稿时长

3 months

期刊介绍： PROTEINS : Structure, Function, and Bioinformatics publishes original reports of significant experimental and analytic research in all areas of protein research: structure, function, computation, genetics, and design. The journal encourages reports that present new experimental or computational approaches for interpreting and understanding data from biophysical chemistry, structural studies of proteins and macromolecular assemblies, alterations of protein structure and function engineered through techniques of molecular biology and genetics, functional analyses under physiologic conditions, as well as the interactions of proteins with receptors, nucleic acids, or other specific ligands or substrates. Research in protein and peptide biochemistry directed toward synthesizing or characterizing molecules that simulate aspects of the activity of proteins, or that act as inhibitors of protein function, is also within the scope of PROTEINS. In addition to full-length reports, short communications (usually not more than 4 printed pages) and prediction reports are welcome. Reviews are typically by invitation; authors are encouraged to submit proposed topics for consideration.