The DOI matches its Crossref record; 40 of the 40 references it cites were found in a registry or an index.
Mfold web server for nucleic acid folding and hybridization prediction
Open accessAbstract
The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences. A variety of 'bulk' servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'.
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.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Traditional methods such as the Zuker algorithm and its derivatives, MFold and ViennaRNA, use dynamic programming to evaluate thermodynamic stability [6], [7], [8].”
From Towards secondary structure prediction of longer mRNA sequences using a quantum-centric optimization scheme (2025) · cites this paper as [7]
Experimental — accuracy not yet measuredIn the citing paper
“Firstly, the majority of the template sequences exhibited a low propensity to form stable secondary structure elements (as judged by mfold26).”
From In-ice evolution of RNA polymerase ribozyme activity (2013) · cites this paper as [26]
In the citing paper
“Mfold analysis (web server for nucleic acid folding and hybridization prediction)27 showed that the clustered 4bp deletions of patients 1, 6 and 8 are located in the stem of the same short hairpin (Supplementary Fig. 2).”
From A SWI/SNF-related autism syndrome caused by de novo mutations in ADNP (2014) · cites this paper as [27]
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
A comprehensive set of sequence analysis programs for the VAX
Devereux, J., Haeberli, P. E., & Smithies, O. (1984) · Nucleic Acids Research · doi:10.1093/nar/12.1part1.387 · Cited by 14,222
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
Self-citationOptimal 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 3,604
Self-citationA unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.
SantaLucia, J. (1998) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.95.4.1460 · Cited by 2,791
Improved Estimation of Secondary Structure in Ribonucleic Acids
Tinoco, I., Borer, P. N., Dengler, B., Levine, M., Uhlenbeck, O. C., Crothers, D. M., & Gralla, J. D. (1973) · Nature New Biology · doi:10.1038/newbio246040a0 · Cited by 2,270
On Finding All Suboptimal Foldings of an RNA Molecule
Zuker, M. (1989) · Science · doi:10.1126/science.2468181 · Cited by 1,998
Self-citationImproved free-energy parameters for predictions of RNA duplex stability.
Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T., & Turner, D. H. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.24.9373 · Cited by 1,470
Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide
Zuker, M., Mathews, D. H., & Turner, D. H. (1999) · Springer eBooks · doi:10.1007/978-94-011-4485-8_2 · Cited by 1,139
Self-citationImproved predictions of secondary structures for RNA.
Jaeger, J. A., Turner, D. H., & Zuker, M. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.20.7706 · Cited by 817
Self-citationStability of ribonucleic acid double-stranded helices
Borer, P. N., Dengler, B., Tinoco, I., & Uhlenbeck, O. C. (1974) · Journal of Molecular Biology · doi:10.1016/0022-2836(74)90357-x · Cited by 762
Research works printed but not linked: 2
- Waterman,M.S. (1978) Secondary structure of single-stranded nucleic acids. In Rota, G.-C. (ed.), Studies in Foundations and Combinatorics number 1 in Advances in Mathematics, Supplementary Studies. Academic Press, NY, pp. 167-212.
- Sankoff,D., Kruskal,J.B., Mainville,S. and Cedergren,R.J. (1983) Fast algorithms to determine RNA secondary structures containing multiple loops. chapter 3. In Sankoff,D. and Kruskal,J.B. (eds), Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, Addison-Wesley Reading, MA, pp. 93-120.
Cited by
Sorted by citations
The HCV Life Cycle: In vitro Tissue Culture Systems and Therapeutic Targets
Gerold, G., & Pietschmann, T. (2014) · Digestive Diseases · doi:10.1159/000360830 · Cited by 4,871
John, B., Enright, A. J., Aravin, A., Tuschl, T., Sander, C., & Marks, D. S. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020363 · Cited by 3,796
A unified classification system for eukaryotic transposable elements
Wicker, T., Sabot, F., Hua‐Van, A., Bennetzen, J. L., Capy, P., Chalhoub, B., Flavell, A. J., Leroy, P., Morgante, M., Panaud, O., et al. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2165 · Cited by 3,159
Efficient genome editing in zebrafish using a CRISPR-Cas system
Hwang, W. Y., Fu, Y., Reyon, D., Maeder, M. L., Tsai, S. Q., Sander, J. D., Peterson, R. T., Yeh, J.-R. J., & Joung, J. K. (2013) · Nature Biotechnology · doi:10.1038/nbt.2501 · Cited by 2,937
Asymmetry in the Assembly of the RNAi Enzyme Complex
Schwarz, D. S., Hutvágner, G., Du, T., Xu, Z., Aronin, N., & Zamore, P. D. (2003) · Cell · doi:10.1016/s0092-8674(03)00759-1 · Cited by 2,922
Metadata
- Authors
- Zuker, M.
- Affiliations
- Rensselaer Polytechnic Institute (US)
- Corresponding author
- Zuker, M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2003-07-01
- Volume
- 31
- Issue
- 13
- Pages
- 3406-3415
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC169194
- OpenAlex
- W2141157874
- Cited by
- 13,404
- References
- 40
- Citations by year
- 2026: 320 · 2025: 487 · 2024: 535 · 2023: 536 · 2022: 575 · 2021: 620 · 2020: 615 · 2019: 625 · 2018: 596 · 2017: 653 · 2016: 634 · 2015: 672 · 2014: 681 · 2013: 716 · 2012: 686
- FWCI
- 151.48
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute of General Medical Sciences (GM54250, R01GM054250)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- RNA secondary structure prediction, single-stranded nucleic acids, web application, graphical user interface
- MeSH terms
- Base Sequence, Computer Graphics, DNA, DNA, Single-Stranded, Models, Molecular, Nucleic Acid Conformation, Nucleic Acid Denaturation, Nucleic Acid Hybridization, RNA, Software, Thermodynamics, User-Computer Interface, Internet, Databases, Nucleic Acid
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
