Sfold

The core RNA secondary structure prediction algorithm is based on rigorous statistical (stochastic) sampling of Boltzmann ensemble of RNA secondary structures, enabling statistical characterization of any local structural features of potential interest to experimental investigators. In a review on nucleic acid structure and prediction,{{Cite journal |last=Zucker |first=M. |date=2000 |title=Calculating nucleic acid secondary structure |journal=Curr. Opin. Struct. Biol. |volume=10 |issue=3 |pages=303–310 |doi=10.1016/s0959-440x(00)00088-9 |pmid=10851192}} the potential of structure sampling described in a prototype algorithm{{Cite journal |last1=Ding |first1=Y. |last2=Lawrence |first2=C. E. |date=1999 |title=A Bayesian Statistical Algorithm for RNA Secondary Structure Prediction |journal=Computers & Chemistry |volume=23 |issue=3–4 |pages=387–400 |doi=10.1016/S0097-8485(99)00010-8|pmid=10404626 }} was highlighted. With the publication of the mature algorithms for Sfold, the sampling approach became the focus of a review{{Cite journal |last=Mathews |first=David H. |date=2006 |title=Revolutions in RNA Secondary Structure Prediction |url=http://dx.doi.org/10.1016/j.jmb.2006.01.067 |journal=Journal of Molecular Biology |volume=359 |issue=3 |pages=526–532 |doi=10.1016/j.jmb.2006.01.067 |pmid=16500677 |issn=0022-2836}} Both the sampling approach and the centroid predictions were discussed in a comprehensive review.{{Citation |last1=Seetin |first1=Matthew G. |title=Bacterial Regulatory RNA |date=2012 |url=http://dx.doi.org/10.1007/978-1-61779-949-5_8 |series=Methods in Molecular Biology |pages=99–122 |access-date=2023-12-05 |place=Totowa, NJ |publisher=Humana Press |isbn=978-1-61779-948-8 |last2=Mathews |first2=David H.|chapter=RNA Structure Prediction: An Overview of Methods |volume=905 |doi=10.1007/978-1-61779-949-5_8 |pmid=22736001 }} As an application module of the Sfold package, the STarMir program{{Cite journal |last1=Rennie |first1=William |last2=Liu |first2=Chaochun |last3=Carmack |first3=C. Steven |last4=Wolenc |first4=Adam |last5=Kanoria |first5=Shaveta |last6=Lu |first6=Jun |last7=Long |first7=Dang |last8=Ding |first8=Ye |date=2014-05-06 |title=STarMir: a web server for prediction of microRNA binding sites |journal=Nucleic Acids Research |volume=42 |issue=W1 |pages=W114–W118 |doi=10.1093/nar/gku376 |issn=1362-4962|doi-access=free |pmid=24803672 |pmc=4086099 }} has been widely used for its capability in modeling target accessibility. STarMir was described in an independent study on microRNA target prediction{{Cite journal |last1=Wong |first1=Leon |last2=You |first2=Zhu-Hong |last3=Guo |first3=Zhen-Hao |last4=Yi |first4=Hai-Cheng |last5=Chen |first5=Zhan-Heng |last6=Cao |first6=Mei-Yuan |date=2020-07-09 |title=MIPDH: A Novel Computational Model for Predicting microRNA–mRNA Interactions by DeepWalk on a Heterogeneous Network |journal=ACS Omega |volume=5 |issue=28 |pages=17022–17032 |doi=10.1021/acsomega.9b04195 |issn=2470-1343|doi-access=free |pmid=32715187 |pmc=7376568 }} STarMir predictions have been used in an attempt to derive improved predictions.{{Cite journal |last1=Ullah |first1=Abu Z.M. Dayem |last2=Sahoo |first2=Sudhakar |last3=Steinhöfel |first3=Kathleen |last4=Albrecht |first4=Andreas A. |date=2012 |title=Derivative scores from site accessibility and ranking of miRNA target predictions |url=http://dx.doi.org/10.1504/ijbra.2012.048966 |journal=International Journal of Bioinformatics Research and Applications |volume=8 |issue=3/4 |pages=171–191 |doi=10.1504/ijbra.2012.048966 |pmid=22961450 |issn=1744-5485}} Predictions by Sfold have led to new biological insights.{{cite journal |last1=Adams |first1=L. |title=Pri-miRNA processing: structure is the key. |journal=Nature Reviews Genetics |date=2017 |volume=18 |issue=3 |page=145 |doi=10.1038/nrg.2017.6 |pmid=28138147|s2cid=30513706 }} The novel ideas of ensemble sampling and centroids have been adopted by others not only for RNA problems, but also for other fundamental problems in computational biology and genomics.{{cite journal |last1=Huang |first1=F. W. |last2=Qin |first2=Jing |last3=Reidys |first3=Christian M |last4=Stadler |first4=Peter F |title=Target prediction and a statistical sampling algorithm for RNA-RNA interaction. |journal=Bioinformatics |date=2009 |volume=26 |issue=2 |pages=175–181 |doi=10.1093/bioinformatics/btp635 |pmid=19910305|pmc=2804298 }}{{cite journal |last1=Harmanchi |first1=Arif Ozgun |last2=Gaurav |first2=Sharma |last3=Mathews |first3=David H |title=Stochastic sampling of the RNA structural alignment space |journal=Nucleic Acids Research |date=2009 |volume=37 |issue=12 |pages=4063–4075 |doi=10.1093/nar/gkp276 |pmid=19429694|pmc=2709569 }}{{cite journal |last1=Hamada |first1=M |last2=Kiryu |first2=H |last3=Mituyama |first3=T |last4=Asai |first4=K |title=Prediction of RNA secondary structure using generalized centroid estimators |journal=Bioinformatics |date=2009 |volume=25 |issue=4 |pages=465–473 |doi=10.1093/bioinformatics/btn601 |pmid=19095700|doi-access=free }}{{cite journal |last1=Carvalho |first1=L. E. |last2=Lawrence |first2=C. E. |title=Centroid estimation in discrete high- dimensional spaces with applications in biology. |journal=Proc Natl Acad Sci |date=2008 |volume=105 |issue=9 |pages=3209–14 |doi=10.1073/pnas.0712329105 |pmid=18305160 |pmc=2265131 |bibcode=2008PNAS..105.3209C |doi-access=free }}{{cite journal |last1=Newberg |first1=L. A. |last2=Thompson |first2=W. A. |last3=Colan |first3=S |last4=Smith |first4=T. M. |last5=McCue |first5=L. A. |last6=Lawrence |first6=C. E. |title=Centroid estimation in discrete high- dimensional spaces with applications in biology. |journal=Bioinformatics |date=2007 |volume=23 |issue=14 |pages=1718–27 |doi=10.1093/bioinformatics/btm241 |pmid=17488758|pmc=2268014 }}

An implementation of stochastic sampling has been included in two widely used RNA software packages, RNA Structure{{cite journal |last1=Bellaousov |first1=S |last2=Reuter |first2=Js |last3=Seetin |first3=MG |last4=Mathews |first4=DH |title=RNAstructure: Web servers for RNA secondary structure prediction and analysis |journal=Nucleic Acids Research |date=2013 |volume=41 |issue=(Web Server Issue) |pages=W471-4 |doi=10.1093/nar/gkt290 |pmid=23620284|doi-access=free |pmc=3692136 }} and the ViennaRNA Package,{{cite journal |last1=Gruber |first1=AR |last2=Lorenz |first2=R |last3=Bernhart |first3=SH |last4=Neuböck |first4=R |last5=Hofacker |first5=IL |title=The Vienna RNA websuite |journal=Nucleic Acids Research |date=2008 |volume=36 |issue=Web Server Issue |pages=W70-4 |doi=10.1093/nar/gkn188 |pmid=18424795|doi-access=free |pmc=2447809 }} which are also based on the Turner RNA thermodynamic parameters.{{cite journal |last1=Mathews |first1=DH |last2=Sabina |first2=J |last3=Turner |first3=DH |title=Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure |journal=J. Mol. Biol. |date=1999 |volume=288 |issue=5 |pages=911–40 |doi=10.1006/jmbi.1999.2700 |pmid=10329189|doi-access=free }} Sfold was featured on a Nucleic Acids Research cover,{{cite journal | url=https://academic.oup.com/nar/article/31/24/7280/2904423 | doi=10.1093/nar/gkg938 | title=A statistical sampling algorithm for RNA secondary structure prediction | date=2003 | last1=Ding | first1=Y. | last2=Lawrence | first2=C. E. | journal=Nucleic Acids Research | volume=31 | issue=24 | pages=7280–7301 | pmid=14654704 | pmc=297010 }} and was highlighted in Science NetWatch.{{cite journal |title=TOOLS: Nucleic Acid Origami |journal=Science |date=2003 |volume=300 |issue=5621 |page=873 |doi=10.1126/science.300.5621.873d|s2cid=220109027 }} The underlying novel model for STarMir was featured in the Cell Biology section of Nature Research Highlights.{{Cite journal |date=2007 |title=Research highlights |journal=Nature |language=en |volume=446 |issue=7136 |pages=586–587 |doi=10.1038/446586a |issn=0028-0836|doi-access=free |bibcode=2007Natur.446..586. }}

Sfold runs on Linux, and is freely available to the scientific community for non-commercial applications, and is available under license for commercial applications. Both the source code and the executables are available at GitHub.

• [https://github.com/Ding-RNA-Lab/Sfold Sfold GitHub repository]
• [https://www.healthresearch.org/sfold-software-for-sirna/ Sfold commercial licensing]
• [https://sfoldrna.github.io Sfold GitHub page]

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Category:Computational biology