The DOI matches its Crossref record; 11 of the 11 references it cites were found in a registry or an index.
CENTROIDFOLD: a web server for RNA secondary structure prediction
Open accessAbstract
The CENTROIDFOLD web server (http://www.ncrna.org/centroidfold/) is a web application for RNA secondary structure prediction powered by one of the most accurate prediction engine. The server accepts two kinds of sequence data: a single RNA sequence and a multiple alignment of RNA sequences. It responses with a prediction result shown as a popular base-pair notation and a graph representation. PDF version of the graph representation is also available. For a multiple alignment sequence, the server predicts a common secondary structure. Usage of the server is quite simple. You can paste a single RNA sequence (FASTA or plain sequence text) or a multiple alignment (CLUSTAL-W format) into the textarea then click on the 'execute CentroidFold' button. The server quickly responses with a prediction result. The major advantage of this server is that it employs our original CentroidFold software as its prediction engine which scores the best accuracy in our benchmark results. Our web server is freely available with no login requirement.
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
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
Zuker, M., & Stiegler, P. (1981) · Nucleic Acids Research · doi:10.1093/nar/9.1.133 · Cited by 3,562
Vienna RNA secondary structure server
Hofacker, I. L. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg599 · Cited by 2,345
The equilibrium partition function and base pair binding probabilities for RNA secondary structure
McCaskill, J. S. (1990) · Biopolymers · doi:10.1002/bip.360290621 · Cited by 1,310
Shukla, S., Mishra, B., Avashthi, H., & Chandra, M. (2022) · Bioinformatics · doi:10.1016/b978-0-323-89775-4.00003-1 · Cited by 1,244
CONTRAfold: RNA secondary structure prediction without physics-based models
Do, C. B., Woods, D. A., & Batzoglou, S. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl246 · Cited by 619
A statistical sampling algorithm for RNA secondary structure prediction
Ding, Y. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg938 · Cited by 566
Pfold: RNA secondary structure prediction using stochastic context-free grammars
Knudsen, B., & Hein, J. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg614 · Cited by 456
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble
DING, Y., CHAN, C. Y., & LAWRENCE, C. E. (2005) · RNA · doi:10.1261/rna.2500605 · Cited by 332
Dowell, R. D., & Eddy, S. R. (2004) · BMC Bioinformatics · doi:10.1186/1471-2105-5-71 · Cited by 280
Prediction of RNA secondary structure using generalized centroid estimators
Hamada, M., Kiryu, H., Sato, K., Mituyama, T., & Asai, K. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btn601 · Cited by 233
Self-citation
Cited by
Getting RIDD of RNA: IRE1 in cell fate regulation
Maurel, M., Chevet, E., Tavernier, J., & Gerlo, S. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.02.008 · Cited by 631
Jeong, D.-H., Park, S., Zhai, J., Gurazada, S. G. R., De Paoli, E., Meyers, B. C., & Green, P. J. (2011) · The Plant Cell · doi:10.1105/tpc.111.089045 · Cited by 334
Aptamers: A Review of Their Chemical Properties and Modifications for Therapeutic Application
Adachi, T., & Nakamura, Y. (2019) · Molecules · doi:10.3390/molecules24234229 · Cited by 300
LinearFold: linear-time approximate RNA folding by 5'-to-3' dynamic programming and beam search
Huang, L., Zhang, H., Deng, D., Zhao, K., Liu, K., Hendrix, D. A., & Mathews, D. H. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz375 · Cited by 207
“, 2006) and CentroidFold (Sato et al., 2009), all use virtually the same dynamic programming (DP) algorithm (Nussinov et al.”
MethodChen, J., Hu, Z., Sun, S., Tan, Q., Wang, Y., Yu, Q., Zong, L., Hong, L., Xiao, J., Shen, T., et al. (2022) · doi:10.1101/2022.08.06.503062 · Cited by 247
Metadata
- Authors
- Sato, K., Hamada, M., Asai, K., & Mituyama, T.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-05-12
- Volume
- 37
- Issue
- Web Server
- Pages
- W277-W280
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2142038007
- Cited by
- 334
- References
- 11
- FWCI
- 4.68
- Type
- journal article
- Language
- en
- Open access
- gold
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: CENTROIDFOLD: a web server for RNA secondary structure prediction. https://app.cochat.ai/papers/10.1093/nar/gkp367
- The paper
- Sato, K., Hamada, M., Asai, K., & Mituyama, T. (2009). CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Research. https://doi.org/10.1093/nar/gkp367
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.
