{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,4]],"date-time":"2025-12-04T01:25:25Z","timestamp":1764811525995,"version":"3.37.3"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2017,7,13]],"date-time":"2017-07-13T00:00:00Z","timestamp":1499904000000},"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":[[2017,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We introduce cgHeliParm, a python program that provides the conformational analysis of Martini-based coarse-grained double strand DNA molecules. The software calculates the helical parameters such as base, base pair and base pair step parameters. cgHeliParm can be used for the analysis of coarse grain Martini molecular dynamics trajectories without transformation into atomistic models.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>This package works with Python 2.7 on MacOS and Linux. The program is freely available for download from https:\/\/github.com\/ifaust83\/cgheliparm. Together with the main script, the base reference files CG_X_std.lib, a number of examples and R scripts are also available from the same website. A tutorial on the use and application is also available at http:\/\/cgmartini.nl\/index.php\/tutorials-general-introduction\/tutorial-martini-dna.<\/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\/btx444","type":"journal-article","created":{"date-parts":[[2017,7,10]],"date-time":"2017-07-10T19:11:16Z","timestamp":1499713876000},"page":"3813-3815","source":"Crossref","is-referenced-by-count":3,"title":["cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations"],"prefix":"10.1093","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7732-1692","authenticated-orcid":false,"given":"Ignacio","family":"Faustino","sequence":"first","affiliation":[{"name":"Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, AG Groningen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S J","family":"Marrink","sequence":"additional","affiliation":[{"name":"Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, AG Groningen, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,7,13]]},"reference":[{"key":"2023020207013913200_btx444-B1","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1002\/wcms.1139","article-title":"Atomistic simulations of nucleosomes","volume":"3","author":"Biswas","year":"2013","journal-title":"WIREs Comput. 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