{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T12:20:17Z","timestamp":1783081217653,"version":"3.54.6"},"reference-count":66,"publisher":"World Scientific Pub Co Pte Ltd","issue":"02","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2013,4]]},"abstract":"<jats:p>Synthetic biology is a rapidly emerging discipline with long-term ramifications that range from single-molecule detection within cells to the creation of synthetic genomes and novel life forms. Truly phenomenal results have been obtained by pioneering groups \u2014 for instance, the combinatorial synthesis of genetic networks, genome synthesis using BioBricks, and hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment, biomolecular self-assembly pathways, etc. Such work strongly suggests that nanotechnology and synthetic biology together seem poised to constitute the most transformative development of the 21st century. In this paper, we present a Constraint Programming (CP) approach to solve the RNA inverse folding problem. Given a target RNA secondary structure, we determine an RNA sequence which folds into the target structure; i.e. whose minimum free energy structure is the target structure. Our approach represents a step forward in RNA design \u2014 we produce the first complete RNA inverse folding approach which allows for the specification of a wide range of design constraints. We also introduce a Large Neighborhood Search approach which allows us to tackle larger instances at the cost of losing completeness, while retaining the advantages of meeting design constraints (motif, GC-content, etc.). Results demonstrate that our software, RNAiFold, performs as well or better than all state-of-the-art approaches; nevertheless, our approach is unique in terms of completeness, flexibility, and the support of various design constraints. The algorithms presented in this paper are publicly available via the interactive webserver http:\/\/bioinformatics.bc.edu\/clotelab\/RNAiFold ; additionally, the source code can be downloaded from that site.<\/jats:p>","DOI":"10.1142\/s0219720013500017","type":"journal-article","created":{"date-parts":[[2012,11,29]],"date-time":"2012-11-29T09:15:25Z","timestamp":1354180525000},"page":"1350001","source":"Crossref","is-referenced-by-count":92,"title":["RNAiFOLD: A CONSTRAINT PROGRAMMING ALGORITHM FOR RNA INVERSE FOLDING AND MOLECULAR DESIGN"],"prefix":"10.1142","volume":"11","author":[{"given":"JUAN ANTONIO","family":"GARCIA-MARTIN","sequence":"first","affiliation":[{"name":"CNB-CSIC, Darwin 3, Campus Cantoblanco, 28049 Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"PETER","family":"CLOTE","sequence":"additional","affiliation":[{"name":"Biology Department, Boston College, 140 Commonwealth Avenue Chestnut Hill, MA, 02467, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"IVAN","family":"DOTU","sequence":"additional","affiliation":[{"name":"Biology Department, Boston College, 140 Commonwealth Avenue Chestnut Hill, MA, 02467, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"219","published-online":{"date-parts":[[2013,4,21]]},"reference":[{"key":"rf1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1001721107"},{"key":"rf2","doi-asserted-by":"publisher","DOI":"10.1186\/1754-1611-2-5"},{"key":"rf3","doi-asserted-by":"publisher","DOI":"10.1145\/366573.366611"},{"key":"rf4","volume-title":"Constraint-Based Local Search","author":"Van Hentenryck P.","year":"2005"},{"key":"rf5","doi-asserted-by":"publisher","DOI":"10.1017\/S1355838299990891"},{"key":"rf6","doi-asserted-by":"publisher","DOI":"10.1007\/PL00006275"},{"key":"rf7","doi-asserted-by":"publisher","DOI":"10.1126\/science.1159689"},{"key":"rf8","doi-asserted-by":"publisher","DOI":"10.1038\/nature05769"},{"key":"rf9","doi-asserted-by":"publisher","DOI":"10.1126\/science.1080372"},{"key":"rf10","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(03)00391-X"},{"key":"rf11","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2007-8-4-210"},{"key":"rf12","doi-asserted-by":"publisher","DOI":"10.1038\/418222a"},{"key":"rf13","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg599"},{"key":"rf14","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-60327-429-6_1"},{"key":"rf15","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0401799101"},{"key":"rf17","doi-asserted-by":"publisher","DOI":"10.1007\/s10601-007-9033-9"},{"key":"rf18","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/25.18.3724"},{"key":"rf19","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2001.5351"},{"key":"rf20","volume":"15","author":"Chang T. 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