The DOI matches its Crossref record; 46 of the 46 references it cites were found in a registry or an index.
Automated de novo prediction of native-like RNA tertiary structures
Open accessAbstract
RNA tertiary structure prediction has been based almost entirely on base-pairing constraints derived from phylogenetic covariation analysis. We describe here a complementary approach, inspired by the Rosetta low-resolution protein structure prediction method, that seeks the lowest energy tertiary structure for a given RNA sequence without using evolutionary information. In a benchmark test of 20 RNA sequences with known structure and lengths of ≈30 nt, the new method reproduces better than 90% of Watson–Crick base pairs, comparable with the accuracy of secondary structure prediction methods. In more than half the cases, at least one of the top five models agrees with the native structure to better than 4 Å rmsd over the backbone. Most importantly, the method recapitulates more than one-third of non-Watson–Crick base pairs seen in the native structures. Tandem stacks of “sheared” base pairs, base triplets, and pseudoknots are among the noncanonical features reproduced in the models. In the cases in which none of the top five models were native-like, higher energy conformations similar to the native structures are still sampled frequently but not assigned low energies. These results suggest that modest improvements in the energy function, together with the incorporation of information from phylogenetic covariance, may allow confident and accurate structure prediction for larger and more complex RNA chains.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Numerical recipes in C: the art of scientific computing
(1993) · Choice Reviews Online · doi:10.5860/choice.30-5638 · Cited by 17,933
Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid
WATSON, J. D., & CRICK, F. H. C. (1953) · Nature · doi:10.1038/171737a0 · Cited by 13,584
Numerical Recipes in C: The Art of Scientific Computing.
Birchenhall, C., Press, W. H., Teukolsky, S. A., Vetterling, W. T., & Flannery, B. P. (1994) · The Economic Journal · doi:10.2307/2234664 · Cited by 4,355
Mathews, D. H., Sabina, J., Zuker, M., & Turner, D. H. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2700 · Cited by 3,795
The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution
Ban, N., Nissen, P., Hansen, J., Moore, P. B., & Steitz, T. A. (2000) · Science · doi:10.1126/science.289.5481.905 · Cited by 3,327
Simons, K. T., Kooperberg, C., Huang, E., & Baker, D. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.0959 · Cited by 1,396
Self-citationXia, T., SantaLucia, J., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C., & Turner, D. H. (1998) · Biochemistry · doi:10.1021/bi9809425 · Cited by 1,140
Geometric nomenclature and classification of RNA base pairs
LEONTIS, N. B., & WESTHOF, E. (2001) · RNA · doi:10.1017/s1355838201002515 · Cited by 1,073
DNA sequence-dependent deformability deduced from protein–DNA crystal complexes
Olson, W. K., Gorin, A. A., Lu, X.-J., Hock, L. M., & Zhurkin, V. B. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.19.11163 · Cited by 1,038
Tinoco, I., & Bustamante, C. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3001 · Cited by 1,010
Cited by
Leaver-Fay (2011) · doi:10.1016/b978-0-12-381270-4.00019-6 · Cited by 1,904
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
Alford, R. F., Leaver-Fay, A., Jeliazkov, J. R., O’Meara, M. J., DiMaio, F. P., Park, H., Shapovalov, M. V., Renfrew, P. D., Mulligan, V. K., Kappel, K., et al. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00125 · Cited by 1,532
Self-citationA triple helix stabilizes the 3′ ends of long noncoding RNAs that lack poly(A) tails
Wilusz, J. E., JnBaptiste, C. K., Lu, L. Y., Kuhn, C.-D., Joshua-Tor, L., & Sharp, P. A. (2012) · Genes & Development · doi:10.1101/gad.204438.112 · Cited by 486
Jonikas, M. A., Radmer, R. J., Laederach, A., Das, R., Pearlman, S., Herschlag, D., & Altman, R. B. (2009) · RNA · doi:10.1261/rna.1270809 · Cited by 316
Self-citation3D RNA and Functional Interactions from Evolutionary Couplings
Weinreb, C., Riesselman, A. J., Ingraham, J. B., Gross, T., Sander, C., & Marks, D. S. (2016) · Cell · doi:10.1016/j.cell.2016.03.030 · Cited by 159
Metadata
- Authors
- Das, R., & Baker, D.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2007-09-11
- Volume
- 104
- Issue
- 37
- Pages
- 14664-14669
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2017838368
- Cited by
- 438
- References
- 46
- FWCI
- 8.26
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Automated de novo prediction of native-like RNA tertiary structures. https://app.cochat.ai/papers/10.1073/pnas.0703836104
- The paper
- Das, R., & Baker, D. (2007). Automated de novo prediction of native-like RNA tertiary structures. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0703836104
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
