{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:49Z","timestamp":1772138089657,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2018,6,20]],"date-time":"2018-06-20T00:00:00Z","timestamp":1529452800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Science","doi-asserted-by":"publisher","award":["P41 GM103313"],"award-info":[{"award-number":["P41 GM103313"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Science","doi-asserted-by":"publisher","award":["P41 GM111135"],"award-info":[{"award-number":["P41 GM111135"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Proteins, especially those involved in signaling pathways are composed of functional modules connected by linker domains with varying degrees of flexibility. To understand the structure\u2013function relationships in these macromolecules, it is helpful to visualize the geometric arrangement of domains. Furthermore, accurate spatial representation of domain structure is necessary for coarse-grain models of the multi-molecular interactions that comprise signaling pathways.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce a new tool, mol2sphere, that transforms the atomistic structure of a macromolecule into a series of linked spheres corresponding to domains. It does this with a k-means clustering algorithm. It may be used for visualization or for coarse grain modeling and simulation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PyMOL plugin, source, and documentation<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>https:\/\/nmrbox.org\/registry\/mol2sphere. SpringSaLaD executables and documentation: http:\/\/vcell.org\/ssalad, SpringSaLaD v.2 source: https:\/\/github.com\/jmasison\/SpringSaLaD.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty487","type":"journal-article","created":{"date-parts":[[2018,6,13]],"date-time":"2018-06-13T15:13:00Z","timestamp":1528902780000},"page":"3948-3950","source":"Crossref","is-referenced-by-count":4,"title":["mol2sphere: spherical decomposition of multi-domain molecules for visualization and coarse grained spatial modeling"],"prefix":"10.1093","volume":"34","author":[{"given":"Joseph","family":"Masison","sequence":"first","affiliation":[{"name":"R. D. Berlin Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA"}]},{"given":"Paul J","family":"Michalski","sequence":"additional","affiliation":[{"name":"R. D. Berlin Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1851-4646","authenticated-orcid":false,"given":"Leslie M","family":"Loew","sequence":"additional","affiliation":[{"name":"R. D. Berlin Center for Cell Analysis and Modeling, UConn Health, Farmington, CT, USA"}]},{"given":"Adam D","family":"Schuyler","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,6,19]]},"reference":[{"key":"2023012712363741500_bty487-B1","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1038\/nmeth.3204","article-title":"cellPACK: a virtual mesoscope to model and visualize structural systems biology","volume":"12","author":"Johnson","year":"2015","journal-title":"Nat. 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