RNA target highlights in CASP15: Evaluation of predicted models by structure providers

Author:

Kretsch Rachael C.1ORCID,Andersen Ebbe S.2ORCID,Bujnicki Janusz M.3ORCID,Chiu Wah145ORCID,Das Rhiju167ORCID,Luo Bingnan8ORCID,Masquida Benoît9ORCID,McRae Ewan K. S.10ORCID,Schroeder Griffin M.1112ORCID,Su Zhaoming8ORCID,Wedekind Joseph E.1112ORCID,Xu Lily13ORCID,Zhang Kaiming14ORCID,Zheludev Ivan N.6ORCID,Moult John15ORCID,Kryshtafovych Andriy16ORCID

Affiliation:

1. Biophysics Program Stanford University School of Medicine Stanford California USA

2. Department of Molecular Biology and Genetics, Interdisciplinary Nanoscience Center Aarhus University Aarhus Denmark

3. International Institute of Molecular and Cell Biology in Warsaw Warsaw Poland

4. Department of Bioengineering, James H. Clark Center Stanford University Stanford California USA

5. Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory Menlo Park California USA

6. Department of Biochemistry Stanford University School of Medicine Stanford California USA

7. Howard Hughes Medical Institute Stanford California USA

8. The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, Department of Geriatrics and National Clinical Research Center for Geriatrics West China Hospital, Sichuan University Chengdu Sichuan China

9. UMR 7156, CNRS—Université de Strasbourg Strasbourg France

10. Center for RNA Therapeutics, Houston Methodist Research Institute Houston Texas USA

11. Department of Biochemistry and Biophysics University of Rochester School of Medicine and Dentistry Rochester New York USA

12. Center for RNA Biology, University of Rochester School of Medicine and Dentistry Rochester New York USA

13. Department of Microbiology and Immunology Stanford University School of Medicine Stanford California USA

14. Division of Life Sciences and Medicine University of Science and Technology of China Hefei China

15. Department of Cell Biology and Molecular Genetics Institute for Bioscience and Biotechnology Research, University of Maryland Rockville Maryland USA

16. Genome Center, University of California, Davis Davis California USA

Abstract

AbstractThe 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.

Funder

Howard Hughes Medical Institute

Ministry of Science and Technology of the People's Republic of China

National Institutes of Health

National Natural Science Foundation of China

National Science Foundation

Novo Nordisk Fonden

Danmarks Frie Forskningsfond

National Institute of General Medical Sciences

Publisher

Wiley

Subject

Molecular Biology,Biochemistry,Structural Biology

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