{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:35:58Z","timestamp":1761863758324},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2017,10,9]],"date-time":"2017-10-09T00:00:00Z","timestamp":1507507200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Many DNA-binding proteins recognize their target sequences indirectly, by sensing DNA\u2019s response to mechanical distortion. ThreaDNA estimates this response based on high-resolution structures of the protein\u2013DNA complex of interest. Implementing an efficient nanoscale modeling of DNA deformations involving essentially no adjustable parameters, it returns the profile of deformation energy along whole genomes, at base-pair resolution, within minutes on usual laptop\/desktop computers. Our predictions can also be easily combined with estimations of direct selectivity through a generalized form of position-weight-matrices. The formalism of ThreaDNA is accessible to a wide audience.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We demonstrate the importance of indirect readout for the nucleosome as well as the bacterial regulators Fis and CRP. Combined with the direct contribution provided by usual sequence motifs, it significantly improves the prediction of sequence selectivity, and allows quantifying the two distinct physical mechanisms underlying it.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Python software available at bioinfo.insa-lyon.fr, natively executable on Linux\/MacOS systems with a user-friendly graphical interface. Galaxy webserver version available.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx634","type":"journal-article","created":{"date-parts":[[2017,10,6]],"date-time":"2017-10-06T19:12:01Z","timestamp":1507317121000},"page":"609-616","source":"Crossref","is-referenced-by-count":12,"title":["ThreaDNA: predicting DNA mechanics\u2019 contribution to sequence selectivity of proteins along whole genomes"],"prefix":"10.1093","volume":"34","author":[{"given":"Jasmin","family":"Cevost","sequence":"first","affiliation":[{"name":"Microbiologie, Adaptation et Pathog\u00e9nie, UMR5240, INSA Lyon, Universit\u00e9 de Lyon, Villeurbanne"}]},{"given":"C\u00e9dric","family":"Vaillant","sequence":"additional","affiliation":[{"name":"Laboratoire de Physique, UMR5672, ENS Lyon, CNRS, Universit\u00e9 de Lyon, Lyon, France"}]},{"given":"Sam","family":"Meyer","sequence":"additional","affiliation":[{"name":"Microbiologie, Adaptation et Pathog\u00e9nie, UMR5240, INSA Lyon, Universit\u00e9 de Lyon, Villeurbanne"}]}],"member":"286","published-online":{"date-parts":[[2017,10,9]]},"reference":[{"key":"2023012712332141600_btx634-B1","doi-asserted-by":"crossref","first-page":"W3","DOI":"10.1093\/nar\/gkw343","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update","volume":"44","author":"Afgan","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023012712332141600_btx634-B2","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1016\/S0006-3495(00)76319-3","article-title":"A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability","volume":"79","author":"Anselmi","year":"2000","journal-title":"Biophys. 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