Filters








22 Hits in 8.2 sec

Asymptotic expected number of base pairs in optimal secondary structure for random RNA using the Nussinov–Jacobson energy model

Peter Clote, Evangelos Kranakis, Danny Krizanc, Ladislav Stacho
<span title="">2007</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lx7dev2le5anbg6oarljwh7lie" style="color: black;">Discrete Applied Mathematics</a> </i> &nbsp;
Motivated by computer experiments, we study asymptotics of the expected maximum number of base pairs in secondary structures for random RNA sequences of length n.  ...  We prove a general theorem entailing the existence of an asymptotic limit for the mean and standard deviation of free energy per nucleotide, as computed by mfold, for random RNA of any fixed compositional  ...  Specifically, we prove the existence of an asymptotic limit for the mean and standard deviation of the minimum free energy (mfe) per nucleotide, as computed either by the Nussinov-Jacobson algorithm [  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.dam.2005.04.022">doi:10.1016/j.dam.2005.04.022</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ubmsr7ouvva3vhmcew3nthcqze">fatcat:ubmsr7ouvva3vhmcew3nthcqze</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190324143602/https://core.ac.uk/download/pdf/82744609.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/77/1d/771d24d18742be1f31bc5446cde83e9d97c0ae2c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.dam.2005.04.022"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Combinatorics of locally optimal RNA secondary structures

Éric Fusy, Peter Clote
<span title="2012-12-22">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kngnkwdthrbili3232uvzfjyyi" style="color: black;">Journal of Mathematical Biology</a> </i> &nbsp;
In the Nussinov energy model, where each base pair contributes −1 towards the energy of the structure, locally optimal structures are exactly the saturated structures, for which we have previously shown  ...  In this paper, we consider the base stacking energy model, a mild variant of the Nussinov model, where each stacked base pair contributes −1 toward the energy of the structure.  ...  In [18] , Hofacker et al. derived a number of asymptotic results on the number of structures, expected number of base pairs, etc. for RNA secondary structures.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00285-012-0631-9">doi:10.1007/s00285-012-0631-9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23263300">pmid:23263300</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/o5qcktpp6rhk3hi3ajbin2yxfu">fatcat:o5qcktpp6rhk3hi3ajbin2yxfu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20130409134242/http://www.lix.polytechnique.fr/~fusy/Articles/RNA.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/17/30/17301f2354647d94995ade084f2b7a4543932b1d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00285-012-0631-9"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy

Yann Ponty
<span title="2007-10-12">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kngnkwdthrbili3232uvzfjyyi" style="color: black;">Journal of Mathematical Biology</a> </i> &nbsp;
Moreover the average-case complexity of the generation is shown to be improved from O(n √ n) to O(n log(n)) in an Boltzmann-weighted homopolymer model based on the Nussinov-Jacobson free-energy model.  ...  We adapt here a surprising technique, the boustrophedon method, to speed up the sampling of RNA secondary structures from the Boltzmann low-energy ensemble.  ...  Acknowledgments The author would like to thank A. Lorenz for reviewing this document and P. Clote for his advise and guidance.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00285-007-0137-z">doi:10.1007/s00285-007-0137-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17932676">pmid:17932676</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ebadyn673bahbk77qhp62ofxba">fatcat:ebadyn673bahbk77qhp62ofxba</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220085047/http://pdfs.semanticscholar.org/25d7/0750fa400e3e1038477e786388f0cf7468d4.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/25/d7/25d70750fa400e3e1038477e786388f0cf7468d4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00285-007-0137-z"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Energy landscape of k-point mutants of an RNA molecule

P. Clote, J. Waldispuhl, B. Behzadi, J.-M. Steyaert
<span title="2005-09-13">2005</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
having least free energy over all secondary structures of all k -point mutants of a given RNA sequence, for k ≤ k.  ...  To understand the effect of pointwise mutation in RNA (Schuster et al., 1994; Clote et al., 2005b) , we consider the distribution of energies of all secondary structures of k-point mutants of a given RNA  ...  While the energy model for RNA in (Waldispühl et al., 2002) is a refinement of the Nussinov-Jacobson energy model (energies for base pairs, rather than stacked base pairs, affine costs given to loops  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bti669">doi:10.1093/bioinformatics/bti669</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16159920">pmid:16159920</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wcmk3cgyhvejlpnzhwhxbc5wzu">fatcat:wcmk3cgyhvejlpnzhwhxbc5wzu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922233639/http://clavius.bc.edu/~clote/pub/RNAmutants.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/37/64/37646751c9512ca407fbf9cd01e436957cca27a5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bti669"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Combinatorics of locally optimal RNA secondary structures [article]

Éric Fusy, Peter Clote
<span title="2012-12-30">2012</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
In the Nussinov energy model, where each base pair contributes -1 towards the energy of the structure, locally optimal structures are exactly the saturated structures, for which we have previously shown  ...  In this paper, we consider the base stacking energy model, a mild variant of the Nussinov model, where each stacked base pair contributes -1 toward the energy of the structure.  ...  Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1112.4610v3">arXiv:1112.4610v3</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pjcdikjj7bh35lipi776kbcvaq">fatcat:pjcdikjj7bh35lipi776kbcvaq</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/arxiv-1112.4610/1112.4610.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1112.4610v3" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Deconvolving RNA Base Pairing Signals [article]

Torin Greenwood, Christine E. Heitsch
<span title="2019-12-15">2019</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Then, we prove under a Nussinov-Jacobson model that a large proportion of RNA structure pairs cannot be jointly reconstructed with low total variation distance.  ...  A growing number of RNA sequences are now known to have distributions of multiple stable sequences.  ...  The Nussinov-Jacobson energy model, based on the algorithm from [21] and analyzed in [22, 23] , assigns energies to structures by totaling the number of base pairs in the structure.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1801.03055v2">arXiv:1801.03055v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/y3oh5f2fazalxjc5rghyvxd5ly">fatcat:y3oh5f2fazalxjc5rghyvxd5ly</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200930183045/https://arxiv.org/pdf/1801.03055v2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4d/52/4d5273f368eb8577dfc8fc80ffa77a786d715b80.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1801.03055v2" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Asymptotic structural properties of quasi-random saturated structures of RNA

Peter Clote, Evangelos Kranakis, Danny Krizanc
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/izdyn6hngbd35czi6err6qypqu" style="color: black;">Algorithms for Molecular Biology</a> </i> &nbsp;
Kinetic traps in the Nussinov energy model are precisely those secondary structures that are saturated, meaning that no base pair can be added without introducing either a pseudoknot or base triple.  ...  RNA folding depends on the distribution of kinetic traps in the landscape of all secondary structures.  ...  Acknowledgements Many thanks to the anonymous referees for useful comments that improved significantly the presentation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1748-7188-8-24">doi:10.1186/1748-7188-8-24</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24156624">pmid:24156624</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3818986/">pmcid:PMC3818986</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/a75vin37u5djnh54tvf3rp2w6y">fatcat:a75vin37u5djnh54tvf3rp2w6y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20131225202327/http://pubmedcentralcanada.ca/pmcc/articles/PMC3818986/pdf/1748-7188-8-24.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e2/2c/e22cafa411228bc428c6ec569e2bd31d3f227847.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1748-7188-8-24"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3818986" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

RNA secondary structures and their prediction

Michael Zuker, David Sankoff
<span title="">1984</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zasl75vjunffjdn7osabykmsua" style="color: black;">Bulletin of Mathematical Biology</a> </i> &nbsp;
Definition of Structure. We number the bases of an RNA sequence from RNA SECONDARY STRUCTURES 593 M. ZUKER AND D. SANKOFF  ...  The emphasis in this approach is on the use of dynamic programming algorithms to minimize free energy. One such algorithm is introduced which comprises existing ones as special cases.  ...  The authors wish to thank B. Shapiro and J. Maizel for their plotting programs used to prepare Figures 1, 3 and 4. Similar thanks are extended to G. Osterburg ( Figure 6 ).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/bf02459506">doi:10.1007/bf02459506</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vbxit4zofjarbccwar44e4lkma">fatcat:vbxit4zofjarbccwar44e4lkma</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20111206134621/http://albuquerque.bioinformatics.uottawa.ca/Papers/JournalPublication/1984_Zuker_Sankoff.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/09/20/0920cb43335d7c84efcdd38a872a4a9ec64e455e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/bf02459506"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Statistical and Bayesian approaches to RNA secondary structure prediction

Y. DING
<span title="2006-03-01">2006</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5r3smv4gwnggfemxt2y4fgjxqa" style="color: black;">RNA: A publication of the RNA Society</a> </i> &nbsp;
This work was supported in part by National Science Foundation grant DMS-0200970 and National Institutes of Health grant GM068726 to Y.D.  ...  The author thanks Clarence Chan for preparing Figure 1 , and Eric Westhof, Dave Mathews, and Steve Carmack for helpful suggestions.  ...  For the simple Nussinov-Jacobson energy model of constant basepair energies (Nussinov and Jacobson 1980) , an efficient algorithm has been developed for computation of the number of structures with k  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1261/rna.2274106">doi:10.1261/rna.2274106</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16495231">pmid:16495231</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1383571/">pmcid:PMC1383571</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3xvhxmnrcnc7bpj5lx5xnwwbyu">fatcat:3xvhxmnrcnc7bpj5lx5xnwwbyu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060927195552/http://sfold.wadsworth.org/Ding_RNA06_review.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/70/c9/70c96e9076dc64a2a1777122505a0dc588fd3370.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1261/rna.2274106"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1383571" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Thermodynamics of RNA structures by Wang-Landau sampling

F. Lou, P. Clote
<span title="2010-06-06">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
In this article, we apply the Wang-Landau (WL) method to compute the density of states for secondary structures of a given RNA sequence, and for hybridizations of two RNA sequences.  ...  Motivation: Thermodynamics-based dynamic programming RNA secondary structure algorithms have been of immense importance in molecular biology, where applications range from the detection of novel selenoproteins  ...  the undocumented option -D of RNAsubopt, which computes the density of states from the enumeration of all secondary structures within a certain energy range of the minimum free energy.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btq218">doi:10.1093/bioinformatics/btq218</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20529917">pmid:20529917</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2881402/">pmcid:PMC2881402</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l53fntfurnhmti4raprveb6m7m">fatcat:l53fntfurnhmti4raprveb6m7m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724194545/https://watermark.silverchair.com/btq218.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAcAwggG8BgkqhkiG9w0BBwagggGtMIIBqQIBADCCAaIGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMwNwWmtODL9ya7SIhAgEQgIIBc9TVEmxGgFSCdrshcC_u0fYK-0gMLGi_J5The4qV1-N74JRx9KdH792F42Zd6Eo9C0YFvBGuocL7M98oerjJci3cu4Bogm8y4vTDnzJWsDPhmt9aO2Vc7vAp_m6QvpoQpfAVrOSDiHgFNm6ikKxrJlCojesfQJhNj-CNk1Ouh6XRjQpjMDi89TyHuT0p0yJCF08m3f_5-wGbjrMxRpY1ciyNy6jWsauYQmDn1oQ8mOTdNBGYzJ1gts6UaH3ke0DUwWf2J7PhTD0OdnIFWfHIn_CspjF2Tz8AtR_-cHjmfHZ-KQgVP6Gs5gIXuDud-02bq693BTOw1Cu5SdmfLhaq14wk5g-ie7-ZLJdL7b1gDhe1AfbyDnCHO6nodlDg3Xp2TiSK3IKAJsmMbk-tfRlGwRwooLRglGnJ4fdb5siPlWjV8173t2iI6WZ40AL0gBXVI7CAQ8BQUAN4V63xygqbu4WRfm_1D0mmzf4LIy7lXGZev1mj" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3f/15/3f1591333e93953d095d063e260454ac57839d5a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btq218"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881402" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Computing the Partition Function for Kinetically Trapped RNA Secondary Structures

William A. Lorenz, Peter Clote, Cynthia Gibas
<span title="2011-01-28">2011</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely  ...  Use of locally optimal structure leads to state-of-the-art secondary structure prediction, as benchmarked against methods involving the computation of minimum free energy and of maximum expected accuracy  ...  A preliminary report of this method was described in the poster paper Q34, ''Calculating Local Optima in the Turner Energy Model for RNA Secondary Structure'', presented by W.A. Lorenz and P.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0016178">doi:10.1371/journal.pone.0016178</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21297972">pmid:21297972</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3030561/">pmcid:PMC3030561</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tcjavsf2wvcqxnbqxy6x3zisrq">fatcat:tcjavsf2wvcqxnbqxy6x3zisrq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170927130939/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0016178&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9b/32/9b32a936c7499d6068ee089bb4365be84c46c99e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0016178"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030561" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

ViennaRNA Package 2.0

Ronny Lorenz, Stephan H Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler, Ivo L Hofacker
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/izdyn6hngbd35czi6err6qypqu" style="color: black;">Algorithms for Molecular Biology</a> </i> &nbsp;
Major changes in the structure of the standard energy model, the Turner 2004 parameters, the pervasive use of multi-core CPUs, and an increasing number of algorithmic variants prompted a major technical  ...  accuracy structures derived from base pairing probabilities, or z-scores for locally stable secondary structures, and support for input in fasta format.  ...  This work was funded, in part, by the austrian GEN-AU projects "regulatory non coding RNA", "Bioinformatics Integration Network III", the Austrian FWF project "SFB F43 RNA regulation of the transcriptome  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1748-7188-6-26">doi:10.1186/1748-7188-6-26</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22115189">pmid:22115189</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3319429/">pmcid:PMC3319429</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xzc4ofhiyndexpodi3n5brv6dy">fatcat:xzc4ofhiyndexpodi3n5brv6dy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180418141045/https://fedora.phaidra.univie.ac.at/fedora/get/o:245869/bdef:Content/download" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/db/ab/dbabbf0525ebae004cedd1d77049201bd22ec3c6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1748-7188-6-26"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319429" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes under Evolutionary Pressure [chapter]

Jérôme Waldispühl, Yann Ponty
<span title="">2011</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
We recently introduced a suite of algorithms called RNAmutants which allows, for the first time, a complete exploration of RNA sequence-structure maps in polynomial time and space.  ...  Indeed, since the Boltzmann probabilities of the mutations depend of the free energy of the structures, RNAmutants has difficulties to sample mutant sequences with low G+C-contents.  ...  Assuming an homopolymer model (any base pair can form), a Nussinov-style energy function and an unconstrained number of mutations, the distribution of the number of G + C is asymptotically normal of mean  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-20036-6_45">doi:10.1007/978-3-642-20036-6_45</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/twx5w52syjfypk2jamjav3mgxy">fatcat:twx5w52syjfypk2jamjav3mgxy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20130629223044/http://hal-polytechnique.archives-ouvertes.fr/docs/00/54/68/47/PDF/paper.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e5/be/e5be2ad41552675f8d4e078df2f3157c2f02e55a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-20036-6_45"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes Under Evolutionary Pressure

Jérôme Waldispühl, Yann Ponty
<span title="">2011</span> <i title="Mary Ann Liebert Inc"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/id6xbd2o6fhy7pts2djgwhtmvy" style="color: black;">Journal of Computational Biology</a> </i> &nbsp;
We recently introduced a suite of algorithms called RNAmutants which allows, for the first time, a complete exploration of RNA sequence-structure maps in polynomial time and space.  ...  Indeed, since the Boltzmann probabilities of the mutations depend of the free energy of the structures, RNAmutants has difficulties to sample mutant sequences with low G+C-contents.  ...  Assuming an homopolymer model (any base pair can form), a Nussinov-style energy function and an unconstrained number of mutations, the distribution of the number of G + C is asymptotically normal of mean  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1089/cmb.2011.0181">doi:10.1089/cmb.2011.0181</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22035326">pmid:22035326</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/awb2fmafnzb6vddtwvmszdak54">fatcat:awb2fmafnzb6vddtwvmszdak54</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20130629223044/http://hal-polytechnique.archives-ouvertes.fr/docs/00/54/68/47/PDF/paper.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e5/be/e5be2ad41552675f8d4e078df2f3157c2f02e55a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1089/cmb.2011.0181"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Folding rate dependence on the chain length for RNA-like heteropolymers

Oxana V Galzitskaya, Alexei V Finkelstein
<span title="">1998</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/i7qhweomhjfebdw6hgy7lr5wly" style="color: black;">Folding &amp; design</a> </i> &nbsp;
Results: Using Monte-Carlo folding simulations for a simple model of RNA secondary structure formation, we estimate the RNA chain length dependence of the time necessary to reach the lowest energy fold  ...  Conclusions: We have obtained a general scaling for the dependence of the RNA secondary structure on the chain length.  ...  is based on the ideas of Nussinov and Jacobson [20] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1359-0278(98)00012-1">doi:10.1016/s1359-0278(98)00012-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/9565751">pmid:9565751</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ftagisq3rzemloabr7vp3e7pdi">fatcat:ftagisq3rzemloabr7vp3e7pdi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190413122445/https://core.ac.uk/download/pdf/82525304.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a7/b8/a7b8c25b0ffb3e135f96ed64f1c5d37bf8beeb02.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1359-0278(98)00012-1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 22 results