{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T17:48:49Z","timestamp":1778608129438,"version":"3.51.4"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Background: Reliable prediction of RNA\u2013RNA binding energies is crucial, e.g. for the understanding on RNAi, microRNA\u2013mRNA binding and antisense interactions. The thermodynamics of such RNA\u2013RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to \u2018open\u2019 the binding site and (2) the energy gained from hybridization.<\/jats:p>\n               <jats:p>Methods: We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired.<\/jats:p>\n               <jats:p>Results: Comparison with experimental data shows that Pu[i, j] can be applied as a significant determinant of local target site accessibility for RNA interference (RNAi). Furthermore, these quantities can be used to rigorously determine binding free energies of short oligomers to large mRNA targets. The resource consumption is comparable with a single partition function computation for the large target molecule. We can show that RNAi efficiency correlates well with the binding energies of siRNAs to their respective mRNA target.<\/jats:p>\n               <jats:p>Availability: \u00a0RNAup will be distributed as part of the Vienna RNA Package,<\/jats:p>\n               <jats:p>Contact: \u00a0ivo@tbi.univie.ac.at<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl024","type":"journal-article","created":{"date-parts":[[2006,1,30]],"date-time":"2006-01-30T01:22:34Z","timestamp":1138584154000},"page":"1177-1182","source":"Crossref","is-referenced-by-count":328,"title":["Thermodynamics of RNA\u2013RNA binding"],"prefix":"10.1093","volume":"22","author":[{"given":"Ulrike","family":"M\u00fcckstein","sequence":"first","affiliation":[{"name":"Institute for Theoretical Chemistry, University of Vienna 1 \u00a0 1 \u00a0 \u00a0 W\u00e4hringerstrasse 17, A-1090 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hakim","family":"Tafer","sequence":"additional","affiliation":[{"name":"Institute for Theoretical Chemistry, University of Vienna 1 \u00a0 1 \u00a0 \u00a0 W\u00e4hringerstrasse 17, A-1090 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00f6rg","family":"Hackerm\u00fcller","sequence":"additional","affiliation":[{"name":"Fraunhofer Institut f\u00fcr Zelltherapie und Immunologie, IZI 2 \u00a0 2 \u00a0 \u00a0 Deutscher Platz 5e, D-04103 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stephan H.","family":"Bernhart","sequence":"additional","affiliation":[{"name":"Institute for Theoretical Chemistry, University of Vienna 1 \u00a0 1 \u00a0 \u00a0 W\u00e4hringerstrasse 17, A-1090 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter F.","family":"Stadler","sequence":"additional","affiliation":[{"name":"Institute for Theoretical Chemistry, University of Vienna 1 \u00a0 1 \u00a0 \u00a0 W\u00e4hringerstrasse 17, A-1090 Vienna, Austria"},{"name":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig 3 \u00a0 3 \u00a0 \u00a0 H\u00e4rtelstrasse 16-18, D-04107 Leipzig, Germany"},{"name":"The Santa Fe Institute 4 \u00a0 4 \u00a0 \u00a0 1399 Hyde Park Rd., Santa Fe, New Mexico"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ivo L.","family":"Hofacker","sequence":"additional","affiliation":[{"name":"Institute for Theoretical Chemistry, University of Vienna 1 \u00a0 1 \u00a0 \u00a0 W\u00e4hringerstrasse 17, A-1090 Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,1,29]]},"reference":[{"key":"2023012408204548400_b1","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1016\/j.jmb.2004.10.082","article-title":"Secondary structure prediction of interacting RNA molecules","volume":"345","author":"Andronescu","year":"2005","journal-title":"J. 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