{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T06:01:38Z","timestamp":1763704898015},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: RNA folding is a complicated kinetic process. The minimum free energy structure provides only a static view of the most stable conformational state of the system. It is insufficient to give detailed insights into the dynamic behavior of RNAs. A sufficiently sophisticated analysis of the folding free energy landscape, however, can provide the relevant information.<\/jats:p>\n               <jats:p>Results: We introduce the Basin Hopping Graph (BHG) as a novel coarse-grained model of folding landscapes. Each vertex of the BHG is a local minimum, which represents the corresponding basin in the landscape. Its edges connect basins when the direct transitions between them are \u2018energetically favorable\u2019. Edge weights endcode the corresponding saddle heights and thus measure the difficulties of these favorable transitions. BHGs can be approximated accurately and efficiently for RNA molecules well beyond the length range accessible to enumerative algorithms.<\/jats:p>\n               <jats:p>Availability and implementation: The algorithms described here are implemented in C++ as standalone programs. Its source code and supplemental material can be freely downloaded from http:\/\/www.tbi.univie.ac.at\/bhg.html .<\/jats:p>\n               <jats:p>Contact: \u00a0qin@bioinf.uni-leipzig.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu156","type":"journal-article","created":{"date-parts":[[2014,3,20]],"date-time":"2014-03-20T03:52:23Z","timestamp":1395287543000},"page":"2009-2017","source":"Crossref","is-referenced-by-count":38,"title":["Basin Hopping Graph: a computational framework to characterize RNA folding landscapes"],"prefix":"10.1093","volume":"30","author":[{"given":"Marcel","family":"Kuchar\u00edk","sequence":"first","affiliation":[{"name":"1 Institute for Theoretical Chemistry and 2 Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria, 3 Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, 1870 Frederiksberg C, Denmark, 4 Department of Computer Science & IZBI & iDiv & LIFE, H\u00e4rtelstra\u00dfe 16-18, D-04107 University of Leipzig, 5 Max Planck Institute for Mathematics in the Sciences and 6 Fraunhofer Institute IZI, Leipzig, Germany, 7 Santa Fe Institute, Santa Fe, NM 87501, USA and 8 Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, Denmark"}]},{"given":"Ivo L.","family":"Hofacker","sequence":"additional","affiliation":[{"name":"1 Institute for Theoretical Chemistry and 2 Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria, 3 Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, 1870 Frederiksberg C, Denmark, 4 Department of Computer Science & IZBI & iDiv & LIFE, H\u00e4rtelstra\u00dfe 16-18, D-04107 University of Leipzig, 5 Max Planck Institute for Mathematics in the Sciences and 6 Fraunhofer Institute IZI, Leipzig, Germany, 7 Santa Fe Institute, Santa Fe, NM 87501, USA and 8 Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, Denmark"},{"name":"1 Institute for Theoretical Chemistry and 2 Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria, 3 Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, 1870 Frederiksberg C, Denmark, 4 Department of Computer Science & IZBI & iDiv & LIFE, H\u00e4rtelstra\u00dfe 16-18, D-04107 University of Leipzig, 5 Max Planck Institute for Mathematics in the Sciences and 6 Fraunhofer Institute IZI, Leipzig, Germany, 7 Santa Fe Institute, Santa Fe, NM 87501, USA and 8 Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, Denmark"},{"name":"1 Institute for Theoretical Chemistry and 2 Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria, 3 Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, 1870 Frederiksberg C, Denmark, 4 Department of Computer Science & IZBI & iDiv & LIFE, H\u00e4rtelstra\u00dfe 16-18, D-04107 University of Leipzig, 5 Max Planck Institute for Mathematics in the Sciences and 6 Fraunhofer Institute IZI, Leipzig, Germany, 7 Santa Fe Institute, Santa Fe, NM 87501, USA and 8 Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, Denmark"}]},{"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[{"name":"1 Institute for Theoretical Chemistry and 2 Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria, 3 Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, 1870 Frederiksberg C, Denmark, 4 Department of Computer Science & IZBI & iDiv & LIFE, H\u00e4rtelstra\u00dfe 16-18, D-04107 University of Leipzig, 5 Max Planck Institute for Mathematics in the Sciences and 6 Fraunhofer Institute IZI, Leipzig, Germany, 7 Santa Fe Institute, Santa Fe, NM 87501, USA and 8 Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, Denmark"},{"name":"1 Institute for Theoretical Chemistry and 2 Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria, 3 Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, 1870 Frederiksberg C, Denmark, 4 Department of Computer Science & IZBI & iDiv & LIFE, H\u00e4rtelstra\u00dfe 16-18, D-04107 University of Leipzig, 5 Max Planck Institute for Mathematics in the Sciences and 6 Fraunhofer Institute IZI, Leipzig, Germany, 7 Santa Fe Institute, Santa Fe, NM 87501, USA and 8 Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, Denmark"},{"name":"1 Institute for Theoretical Chemistry and 2 Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria, 3 Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, 1870 Frederiksberg C, Denmark, 4 Department of Computer Science & IZBI & iDiv & LIFE, H\u00e4rtelstra\u00dfe 16-18, D-04107 University of Leipzig, 5 Max Planck Institute for Mathematics in the Sciences and 6 Fraunhofer Institute IZI, Leipzig, Germany, 7 Santa Fe Institute, Santa Fe, NM 87501, USA and 8 Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, Denmark"},{"name":"1 Institute for Theoretical Chemistry and 2 Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria, 3 Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, 1870 Frederiksberg C, Denmark, 4 Department of Computer Science & IZBI & iDiv & LIFE, H\u00e4rtelstra\u00dfe 16-18, D-04107 University of Leipzig, 5 Max Planck Institute for Mathematics in the Sciences and 6 Fraunhofer Institute IZI, Leipzig, Germany, 7 Santa Fe Institute, Santa Fe, NM 87501, USA and 8 Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, Denmark"},{"name":"1 Institute for Theoretical Chemistry and 2 Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria, 3 Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, 1870 Frederiksberg C, Denmark, 4 Department of Computer Science & IZBI & iDiv & LIFE, H\u00e4rtelstra\u00dfe 16-18, D-04107 University of Leipzig, 5 Max Planck Institute for Mathematics in the Sciences and 6 Fraunhofer Institute IZI, Leipzig, Germany, 7 Santa Fe Institute, Santa Fe, NM 87501, USA and 8 Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, Denmark"}]},{"given":"Jing","family":"Qin","sequence":"additional","affiliation":[{"name":"1 Institute for Theoretical Chemistry and 2 Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria, 3 Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, 1870 Frederiksberg C, Denmark, 4 Department of Computer Science & IZBI & iDiv & LIFE, H\u00e4rtelstra\u00dfe 16-18, D-04107 University of Leipzig, 5 Max Planck Institute for Mathematics in the Sciences and 6 Fraunhofer Institute IZI, Leipzig, Germany, 7 Santa Fe Institute, Santa Fe, NM 87501, USA and 8 Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, Denmark"},{"name":"1 Institute for Theoretical Chemistry and 2 Research group BCB, Faculty of Computer Science, University of Vienna, W\u00e4hringer Stra\u00dfe 17, 1090 Vienna, Austria, 3 Center for non-coding RNA in Technology and Health, University of Copenhagen, Gr\u00f8nneg\u00e5rdsvej 3, 1870 Frederiksberg C, Denmark, 4 Department of Computer Science & IZBI & iDiv & LIFE, H\u00e4rtelstra\u00dfe 16-18, D-04107 University of Leipzig, 5 Max Planck Institute for Mathematics in the Sciences and 6 Fraunhofer Institute IZI, Leipzig, Germany, 7 Santa Fe Institute, Santa Fe, NM 87501, USA and 8 Department of Mathematics and Computer Science, University Of Southern Denmark, Odense, Denmark"}]}],"member":"286","published-online":{"date-parts":[[2014,3,19]]},"reference":[{"key":"2023012711275022700_btu156-B1","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1093\/emboj\/16.3.599","article-title":"Viroid processing: Switch from cleavage to ligation is driven by a change from a tetraloop to a loop E conformation","volume":"16","author":"Baumstark","year":"1997","journal-title":"EMBO J."},{"key":"2023012711275022700_btu156-B2","doi-asserted-by":"crossref","first-page":"5129","DOI":"10.1002\/j.1460-2075.1992.tb05620.x","article-title":"In vitro\n               recombination and terminal elongation of RNA by Q\u03b2 replicase","volume":"38","author":"Biebricher","year":"1992","journal-title":"EMBO J."},{"key":"2023012711275022700_btu156-B3","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1089\/cmb.2005.12.83","article-title":"An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model","volume":"1","author":"Clote","year":"2005","journal-title":"J. Comput. Biol."},{"key":"2023012711275022700_btu156-B4","doi-asserted-by":"crossref","first-page":"1974","DOI":"10.1093\/bioinformatics\/btp250","article-title":"VARNA: interactive drawing and editing of the RNA secondary structure","volume":"25","author":"Darty","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012711275022700_btu156-B5","doi-asserted-by":"crossref","first-page":"14664","DOI":"10.1073\/pnas.0703836104","article-title":"Automated de novo prediction of native-like RNA tertiary structures","volume":"104","author":"Das","year":"2007","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012711275022700_btu156-B6","doi-asserted-by":"crossref","first-page":"7280","DOI":"10.1093\/nar\/gkg938","article-title":"A statistical sampling algorithm for RNA secondary structure prediction","volume":"31","author":"Ding","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012711275022700_btu156-B7","doi-asserted-by":"crossref","first-page":"W135","DOI":"10.1093\/nar\/gkh449","article-title":"Sfold web server for statistical folding and rational design of nucleic acids","volume":"32","author":"Ding","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012711275022700_btu156-B8","doi-asserted-by":"crossref","first-page":"1711","DOI":"10.1093\/nar\/gkp1054","article-title":"Computing folding pathways between RNA secondary structures","volume":"38","author":"Dotu","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012711275022700_btu156-B9","doi-asserted-by":"crossref","first-page":"8417","DOI":"10.1063\/1.480217","article-title":"Evolution of the potential energy surface with size for Lennard-Jones clusters","volume":"111","author":"Doye","year":"1999","journal-title":"J. Chem. Phys."},{"key":"2023012711275022700_btu156-B10","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1017\/S1355838200992161","article-title":"RNA folding kinetics at elementary step resolution","volume":"6","author":"Flamm","year":"2000","journal-title":"RNA"},{"key":"2023012711275022700_btu156-B11","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1524\/zpch.2002.216.2.155","article-title":"Barrier trees of degenerate landscapes","volume":"216","author":"Flamm","year":"2002","journal-title":"Z. Phys. Chem."},{"key":"2023012711275022700_btu156-B12","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1007\/s00285-012-0631-9","article-title":"Combinatorics of locally optimal RNA secondary structures","volume":"68","author":"Fusy","year":"2012","journal-title":"J. Math. Biology,"},{"key":"2023012711275022700_btu156-B13","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1137\/S0895480199355225","article-title":"Efficiency of local search with multiple local optima","volume":"15","author":"Garnier","year":"2000","journal-title":"SIAM J. Discrete Math."},{"key":"2023012711275022700_btu156-B14","doi-asserted-by":"crossref","first-page":"3219","DOI":"10.1103\/PhysRevE.60.3219","article-title":"Energy landscapes, supergraphs, and \u201cfolding funnels\u201d in spin systems","volume":"60","author":"Garstecki","year":"1999","journal-title":"Phys. Rev. E"},{"key":"2023012711275022700_btu156-B15","doi-asserted-by":"crossref","first-page":"3429","DOI":"10.1093\/nar\/gkg599","article-title":"Vienna RNA secondary structure server","volume":"31","author":"Hofacker","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012711275022700_btu156-B16","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/S0166-218X(98)00073-0","article-title":"Combinatorics of RNA secondary structures","volume":"88","author":"Hofacker","year":"1996","journal-title":"Discrete Appl. Math"},{"key":"2023012711275022700_btu156-B17","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/BF00818163","article-title":"Fast folding and comparison of RNA secondary structures","volume":"125","author":"Hofacker","year":"1994","journal-title":"Monatsh. Chem."},{"key":"2023012711275022700_btu156-B18","doi-asserted-by":"crossref","first-page":"6515","DOI":"10.1073\/pnas.110533697","article-title":"Modeling RNA folding paths with pseudoknots: application to hepatitis delta virus ribozyme","volume":"97","author":"Isambert","year":"2000","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012711275022700_btu156-B19","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1007\/978-3-642-41888-4_6","volume-title":"Recent Advances in the Theory and Application of Fitness Landscapes","author":"Klemm","year":"2014"},{"key":"2023012711275022700_btu156-B20","doi-asserted-by":"crossref","first-page":"2661","DOI":"10.1007\/s00018-009-0041-3","article-title":"Microbial thermosensors","volume":"66","author":"Klinkert","year":"2009","journal-title":"Cell. Mol. Life Sci."},{"key":"2023012711275022700_btu156-B21","doi-asserted-by":"crossref","first-page":"L95","DOI":"10.1088\/0305-4470\/27\/4\/001","article-title":"\u201cValley Structures\u201d in the phase space of a finite 3D Ising spin glass with \u00b1\n              i\n               interactions","volume":"27","author":"Klotz","year":"1994","journal-title":"J. Phys. A Math. Gen."},{"key":"2023012711275022700_btu156-B22","first-page":"11","article-title":"2D projections of RNA folding landscapes","volume-title":"GCB.LNI","author":"Lorenz","year":"2009"},{"key":"2023012711275022700_btu156-B23","first-page":"26","article-title":"ViennaRNA Package 2.0","volume":"6","author":"Lorenz","year":"2011","journal-title":"Alg. Mol. Biol."},{"key":"2023012711275022700_btu156-B24","doi-asserted-by":"crossref","first-page":"e16178","DOI":"10.1371\/journal.pone.0016178","article-title":"Computing the partition function for kinetically trapped RNA secondary structures","volume":"6","author":"Lorenz","year":"2011","journal-title":"PLoS One"},{"key":"2023012711275022700_btu156-B25","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1006\/jmbi.1999.2700","article-title":"Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure","volume":"288","author":"Mathews","year":"1999","journal-title":"J. Mol. Biol."},{"key":"2023012711275022700_btu156-B26","doi-asserted-by":"crossref","first-page":"7287","DOI":"10.1073\/pnas.0401799101","article-title":"Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure","volume":"101","author":"Mathews","year":"2004","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012711275022700_btu156-B27","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1007\/s11047-010-9239-4","article-title":"NP-completeness of the energy barrier problem without pseudoknots and temporary arcs","volume":"10","author":"Ma\u0148uch","year":"2011","journal-title":"Nat. Comput."},{"key":"2023012711275022700_btu156-B28","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1002\/bip.360290621","article-title":"The equilibrium partition function and base pair binding probabilities for RNA secondary structure","volume":"29","author":"McCaskill","year":"1990","journal-title":"Biopolymers"},{"key":"2023012711275022700_btu156-B29","doi-asserted-by":"crossref","first-page":"3153","DOI":"10.1088\/0305-4470\/31\/14\/005","article-title":"Barrier heights between ground states in a model of RNA secondary structure","volume":"31","author":"Morgan","year":"1998","journal-title":"J. Phys. A Math. Gen."},{"key":"2023012711275022700_btu156-B30","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1111\/j.1574-6976.2005.004.x","article-title":"RNA thermometers","volume":"30","author":"Narberhaus","year":"2006","journal-title":"FEMS Microbiol. Rev."},{"key":"2023012711275022700_btu156-B31","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1006\/jmbi.1998.1798","article-title":"A toggle duplex in hepatitis delta virus self-cleaving RNA that stabilizes an inactive and a salt-dependent pro-active ribozyme conformation","volume":"279","author":"Perrotta","year":"1998","journal-title":"J. Mol. Biol."},{"key":"2023012711275022700_btu156-B32","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1007\/s00285-007-0137-z","article-title":"Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy: the boustrophedon method","volume":"56","author":"Ponty","year":"2008","journal-title":"J. Math. Biol."},{"key":"2023012711275022700_btu156-B33","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1137\/S0036144501395952","article-title":"Combinatorial landscapes","volume":"44","author":"Reidys","year":"2002","journal-title":"SIAM Rev."},{"key":"2023012711275022700_btu156-B34","doi-asserted-by":"crossref","first-page":"2053","DOI":"10.1006\/jmbi.1998.2436","article-title":"A dynamic programming algorithm for RNA structure prediction including pseudoknots","volume":"285","author":"Rivas","year":"1999","journal-title":"J. Mol. Biol."},{"key":"2023012711275022700_btu156-B35","doi-asserted-by":"crossref","first-page":"2325","DOI":"10.1007\/s00894-010-0951-x","article-title":"RNA and protein 3D structure modeling: similarities and differences","volume":"17","author":"Rother","year":"2011","journal-title":"J. Mol. Model."},{"key":"2023012711275022700_btu156-B36","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1093\/bioinformatics\/btr715","article-title":"Approximating the set of local minima in partial RNA folding landscapes","volume":"28","author":"Sahoo","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012711275022700_btu156-B37","doi-asserted-by":"crossref","first-page":"448","DOI":"10.1126\/science.289.5478.448","article-title":"One sequence, two ribozymes: implications for the emergence of new ribozyme folds","volume":"289","author":"Schultes","year":"2000","journal-title":"Science"},{"key":"2023012711275022700_btu156-B38","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/S0010-4655(98)00176-3","article-title":"The lid method for exhaustive exploration of metastable states of complex systems","volume":"116","author":"Sibani","year":"1999","journal-title":"Comput. Phys. Commun."},{"key":"2023012711275022700_btu156-B39","doi-asserted-by":"crossref","first-page":"1378","DOI":"10.1093\/nar\/gkn987","article-title":"RNA structure prediction from evolutionary patterns of nucleotide composition","volume":"37","author":"Smit","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023012711275022700_btu156-B40","doi-asserted-by":"crossref","first-page":"3339","DOI":"10.1093\/nar\/gkm101","article-title":"Evolutionary rates vary among rRNA structural elements","volume":"35","author":"Smit","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023012711275022700_btu156-B41","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1016\/j.jmb.2008.02.007","article-title":"Simulating RNA folding kinetics on approximated energy landscapes","volume":"381","author":"Tang","year":"2008","journal-title":"J. Mol. Biol."},{"key":"2023012711275022700_btu156-B42","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1146\/annurev.physchem.52.1.751","article-title":"Early events in RNA folding","volume":"52","author":"Thirumalai","year":"2001","journal-title":"Annu. Rev. Phys. Chem."},{"key":"2023012711275022700_btu156-B43","doi-asserted-by":"crossref","first-page":"2877","DOI":"10.1098\/rsta.2011.0208","article-title":"Decoding the energy landscape: extracting structure, dynamics and thermodynamics","volume":"370","author":"Wales","year":"2011","journal-title":"Phil. Trans. R. Soc. A"},{"key":"2023012711275022700_btu156-B44","doi-asserted-by":"crossref","first-page":"4731","DOI":"10.1088\/0305-4470\/37\/17\/005","article-title":"Exact folding dynamics of RNA secondary structures","volume":"37","author":"Wolfinger","year":"2004","journal-title":"J. Phys. A Math. Gen."},{"key":"2023012711275022700_btu156-B45","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1002\/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G","article-title":"Complete suboptimal folding of RNA and the stability of secondary structures","volume":"49","author":"Wuchty","year":"1999","journal-title":"Biopolymers"},{"key":"2023012711275022700_btu156-B46","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1093\/nar\/gkl1036","article-title":"Encoding folding paths of RNA switches","volume":"35","author":"Xayaphoummine","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023012711275022700_btu156-B47","doi-asserted-by":"crossref","first-page":"3406","DOI":"10.1093\/nar\/gkg595","article-title":"Mfold web server for nucleic acid folding and hybridization prediction","volume":"31","author":"Zuker","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012711275022700_btu156-B48","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1016\/S0092-8240(84)80062-2","article-title":"RNA secondary structures and their prediction","volume":"46","author":"Zuker","year":"1984","journal-title":"Bull. Math. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/14\/2009\/48925837\/bioinformatics_30_14_2009.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/14\/2009\/48925837\/bioinformatics_30_14_2009.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T11:56:45Z","timestamp":1674820605000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/14\/2009\/2390590"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,3,19]]},"references-count":48,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2014,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu156","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,7,15]]},"published":{"date-parts":[[2014,3,19]]}}}