{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T20:38:08Z","timestamp":1775680688721,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2019,2,19]],"date-time":"2019-02-19T00:00:00Z","timestamp":1550534400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Sven and Lilly Lawskis Foundation"},{"DOI":"10.13039\/501100004063","name":"Knut and Alice Wallenberg foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004063","id-type":"DOI","asserted-by":"crossref"}]},{"name":"KAW"},{"name":"Vetenskapsr\u00e5det and the Swedish e-Science Research Center"},{"name":"Swedish National Infrastructure for Computing"},{"name":"SNIC"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Understanding how proteins transition between different conformers, and how conformers relate to each other in terms of structure and function, is not trivial. Here, we present an online tool for transition pathway generation between two protein conformations using Elastic Network Driven Brownian Dynamics Importance Sampling, a coarse-grained simulation algorithm, which spontaneously predicts transition intermediates trapped experimentally. In addition to path-generation, the server provides an interactive 2D-motion landscape graphical representation of the transitions or any additional conformers to explore their structural relationships.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>eBDIMS is available online: http:\/\/ebdims.biophysics.se\/ or as standalone software: https:\/\/github.com\/laura-orellana\/eBDIMS, https:\/\/github.com\/cabergh\/eBDIMS.<\/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\/btz104","type":"journal-article","created":{"date-parts":[[2019,2,18]],"date-time":"2019-02-18T04:25:53Z","timestamp":1550463953000},"page":"3505-3507","source":"Crossref","is-referenced-by-count":28,"title":["eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces"],"prefix":"10.1093","volume":"35","author":[{"given":"Laura","family":"Orellana","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University , Stockholm, Sweden"}]},{"given":"Johan","family":"Gustavsson","sequence":"additional","affiliation":[{"name":"Department of Computational Science and Technology, KTH Royal Institute of Technology , Stockholm, Sweden"}]},{"given":"Cathrine","family":"Bergh","sequence":"additional","affiliation":[{"name":"Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology , Solna, Sweden"}]},{"given":"Ozge","family":"Yoluk","sequence":"additional","affiliation":[{"name":"Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology , Solna, Sweden"}]},{"given":"Erik","family":"Lindahl","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University , Stockholm, Sweden"},{"name":"Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology , Solna, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2019,2,19]]},"reference":[{"key":"2023013108052655400_btz104-B1","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1093\/bioinformatics\/btr168","article-title":"ProDy: protein dynamics inferred from theory and experiments","volume":"27","author":"Bakan","year":"2011","journal-title":"Bioinformatics"},{"key":"2023013108052655400_btz104-B2","doi-asserted-by":"crossref","first-page":"2695","DOI":"10.1093\/bioinformatics\/btl461","article-title":"Bio3d: an R package for the comparative analysis of protein structures","volume":"22","author":"Grant","year":"2006","journal-title":"Bioinformatics"},{"key":"2023013108052655400_btz104-B3","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.sbi.2015.11.013","article-title":"New generation of elastic network models","volume":"37","author":"L\u00f3pez-Blanco","year":"2016","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023013108052655400_btz104-B4","doi-asserted-by":"crossref","first-page":"2910","DOI":"10.1021\/ct100208e","article-title":"Approaching elastic network models to molecular dynamics flexibility","volume":"6","author":"Orellana","year":"2010","journal-title":"J. Chem. Theory Comput."},{"key":"2023013108052655400_btz104-B5","doi-asserted-by":"crossref","first-page":"12575","DOI":"10.1038\/ncomms12575","article-title":"Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations","volume":"7","author":"Orellana","year":"2016","journal-title":"Nat. Commun."},{"key":"2023013108052655400_btz104-B6","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/B978-0-12-386485-7.00005-3","article-title":"Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings","volume":"85","author":"Orozco","year":"2011","journal-title":"Adv. Protein Chem. Struct. 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