@article{283fa2c1b3114c03a7338e6c02298ba1,
title = "RNA target highlights in CASP15: Evaluation of predicted models by structure providers",
abstract = "The first RNA category of the Critical Assessment of Techniques for Structure Prediction competition was only made possible because of the scientists who provided experimental structures to challenge the predictors. In this article, these scientists offer a unique and valuable analysis of both the successes and areas for improvement in the predicted models. All 10 RNA-only targets yielded predictions topologically similar to experimentally determined structures. For one target, experimentalists were able to phase their x-ray diffraction data by molecular replacement, showing a potential application of structure predictions for RNA structural biologists. Recommended areas for improvement include: enhancing the accuracy in local interaction predictions and increased consideration of the experimental conditions such as multimerization, structure determination method, and time along folding pathways. The prediction of RNA–protein complexes remains the most significant challenge. Finally, given the intrinsic flexibility of many RNAs, we propose the consideration of ensemble models.",
keywords = "CASP, RNA folding, RNA structure prediction, community-wide experiment, cryo-EM, x-ray crystallography, Proteins/chemistry, X-Ray Diffraction, Models, Molecular, Protein Conformation, Computational Biology/methods",
author = "Kretsch, {Rachael C.} and Andersen, {Ebbe S.} and Bujnicki, {Janusz M.} and Wah Chiu and Rhiju Das and Bingnan Luo and Beno{\^i}t Masquida and McRae, {Ewan K.S.} and Schroeder, {Griffin M.} and Zhaoming Su and Wedekind, {Joseph E.} and Lily Xu and Kaiming Zhang and Zheludev, {Ivan N.} and John Moult and Andriy Kryshtafovych",
note = "Funding Information: This work was supported by Stanford BioX (Bowes Graduate Student Fellowship to Rachael C. Kretsch, Interdisciplinary Initiative Program to Rhiju Das), the National Institutes of Health (R35 GM122579 to Rhiju Das, R01-GM06316preQ12 to Joseph E. Wedekind, T32-GM118283 to Griffin M. Schroeder), Howard Hughes Medical Institute (to Rhiju Das), the National Science Foundation (GRFP DGE-1656518 to Lily Xu), Ministry of Science and Technology of China (2022YFC2303700 and 2021YFA1301900 to Zhaoming Su), the National Natural Science Foundation of China (32222040 and 32070049 to Zhaoming Su), the US National Institute of General Medical Sciences (NIGMS/NIH R01GM100482 to Andriy Kryshtafovych), the National Science Centre, Poland (NCN, 2017/26/A/NZ1/01083 to Janusz M. Bujnicki), Elon Huntington Hooker Fellowship (to Griffin M. Schroeder), the Interdisciplinary Thematic Institute IMCBio of the ITI 2021-2028 program at the University of Strasbourg, CNRS, and Inserm by IdEx Unistra (ANR-10-IDEX-0002 to Beno{\^i}t Masquida), and under the framework of the French Investments Program for the Future EUR (IMCBio ANR-17-EUR-0023 to Beno{\^i}t Masquida), Independent Research Fund Denmark (9040-00425B to Ebbe S. Andersen), Novo Nordisk Foundation (NNF21OC0070452 to Ebbe S. Andersen), the Canadian Natural Sciences and Engineering Research Council (532417 to Ewan K. S. McRae), and the Houston Methodist Research Institute and the Center for RNA Therapeutics (Ewan K. S. McRae). For the work of Griffin M. Schroeder and Joseph E. Wedekind, the use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the US Department of Energy, Office of Basic Energy Sciences (DE-AC02-76SF00515); the SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research and by the National Institutes of Health, National Institute of General Medical Sciences (P41 GM103393). Beno{\^i}t Masquida thanks Eric Westhof for critical reading of Section 2.1. This article is subject to HHMI's Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author-accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication. Funding Information: This work was supported by Stanford BioX (Bowes Graduate Student Fellowship to Rachael C. Kretsch, Interdisciplinary Initiative Program to Rhiju Das), the National Institutes of Health (R35 GM122579 to Rhiju Das, R01‐GM06316preQ12 to Joseph E. Wedekind, T32‐GM118283 to Griffin M. Schroeder), Howard Hughes Medical Institute (to Rhiju Das), the National Science Foundation (GRFP DGE‐1656518 to Lily Xu), Ministry of Science and Technology of China (2022YFC2303700 and 2021YFA1301900 to Zhaoming Su), the National Natural Science Foundation of China (32222040 and 32070049 to Zhaoming Su), the US National Institute of General Medical Sciences (NIGMS/NIH R01GM100482 to Andriy Kryshtafovych), the National Science Centre, Poland (NCN, 2017/26/A/NZ1/01083 to Janusz M. Bujnicki), Elon Huntington Hooker Fellowship (to Griffin M. Schroeder), the Interdisciplinary Thematic Institute IMCBio of the ITI 2021‐2028 program at the University of Strasbourg, CNRS, and Inserm by IdEx Unistra (ANR‐10‐IDEX‐0002 to Beno{\^i}t Masquida), and under the framework of the French Investments Program for the Future EUR (IMCBio ANR‐17‐EUR‐0023 to Beno{\^i}t Masquida), Independent Research Fund Denmark (9040‐00425B to Ebbe S. Andersen), Novo Nordisk Foundation (NNF21OC0070452 to Ebbe S. Andersen), the Canadian Natural Sciences and Engineering Research Council (532417 to Ewan K. S. McRae), and the Houston Methodist Research Institute and the Center for RNA Therapeutics (Ewan K. S. McRae). For the work of Griffin M. Schroeder and Joseph E. Wedekind, the use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the US Department of Energy, Office of Basic Energy Sciences (DE‐AC02‐76SF00515); the SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research and by the National Institutes of Health, National Institute of General Medical Sciences (P41 GM103393). Beno{\^i}t Masquida thanks Eric Westhof for critical reading of Section 2.1 . This article is subject to HHMI's Open Access to Publications policy. HHMI lab heads have previously granted a nonexclusive CC BY 4.0 license to the public and a sublicensable license to HHMI in their research articles. Pursuant to those licenses, the author‐accepted manuscript of this article can be made freely available under a CC BY 4.0 license immediately upon publication. Publisher Copyright: {\textcopyright} 2023 The Authors. Proteins: Structure, Function, and Bioinformatics published by Wiley Periodicals LLC.",
year = "2023",
month = dec,
doi = "10.1002/prot.26550",
language = "English (US)",
volume = "91",
pages = "1600--1615",
journal = "Proteins: Structure, Function and Bioinformatics",
issn = "0887-3585",
publisher = "Wiley",
number = "12",
}