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Kretsch RC, Albrecht R, Andersen ES, Chen HA, Chiu W, Das R, Gezelle JG, Hartmann MD, Höbartner C, Hu Y, Jadhav S, Johnson PE, Jones CP, Koirala D, Kristoffersen EL, Largy E, Lewicka A, Mackereth CD, Marcia M, Nigro M, Ojha M, Piccirilli JA, Rice PA, Shin H, Steckelberg AL, Su Z, Srivastava Y, Wang L, Wu Y, Xie J, Zwergius NH, Moult J, Kryshtafovych A
bioRxiv - (-) - [2025-04-18; online 2025-04-18]
Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular. Here, we report quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs, however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non-canonical regions where, e.g., the nucleic-acid backbone bends or a base forms a non-standard hydrogen bond. These bends and non-canonical interactions are integral to form functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life-cycle, posing a future challenge for the community.
PubMed 40568131
DOI 10.1101/2025.04.15.649049
Crossref 10.1101/2025.04.15.649049
pmc: PMC12191101
pii: 2025.04.15.649049