{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T06:02:29Z","timestamp":1763704949401},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,11,14]],"date-time":"2016-11-14T00:00:00Z","timestamp":1479081600000},"content-version":"vor","delay-in-days":915,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Energy landscapes provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions. Higher abstraction levels based on a macro-state decomposition of the landscape enable the study of larger systems; however, they are still restricted by huge memory requirements of exact approaches.<\/jats:p>\n               <jats:p>Results: We present a highly parallelizable local enumeration scheme that enables the computation of exact macro-state transition models with highly reduced memory requirements. The approach is evaluated on RNA secondary structure landscapes using a gradient basin definition for macro-states. Furthermore, we demonstrate the need for exact transition models by comparing two barrier-based approaches, and perform a detailed investigation of gradient basins in RNA energy landscapes.<\/jats:p>\n               <jats:p>Availability and implementation: Source code is part of the C++ Energy Landscape Library available at http:\/\/www.bioinf.uni-freiburg.de\/Software\/ .<\/jats:p>\n               <jats:p>Contact: \u00a0mmann@informatik.uni-freiburg.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu337","type":"journal-article","created":{"date-parts":[[2014,5,16]],"date-time":"2014-05-16T01:21:59Z","timestamp":1400203319000},"page":"2584-2591","source":"Crossref","is-referenced-by-count":11,"title":["Memory-efficient RNA energy landscape exploration"],"prefix":"10.1093","volume":"30","author":[{"given":"Martin","family":"Mann","sequence":"first","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, 2 Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, 3 Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and 4 Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria"}]},{"given":"Marcel","family":"Kuchar\u00edk","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, 2 Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, 3 Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and 4 Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria"}]},{"given":"Christoph","family":"Flamm","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, 2 Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, 3 Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and 4 Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria"}]},{"given":"Michael T.","family":"Wolfinger","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, 2 Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, 3 Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and 4 Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria"},{"name":"1 Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, 2 Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, 3 Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and 4 Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria"},{"name":"1 Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, 2 Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, 3 Center for Integrative Bioinformatics Vienna, Max F. 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