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'.
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“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]
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“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]
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“Traditional methods such as the Zuker algorithm and its derivatives, MFold and ViennaRNA, use dynamic programming to evaluate thermodynamic stability [6], [7], [8].”
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
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