{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T08:01:59Z","timestamp":1790755319413,"version":"4.1.0"},"reference-count":56,"publisher":"Wiley","issue":"25","license":[{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[2026,9,30]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Protein conformational motion depends on geometric and chemical constraints in side\u2010chain packing. Thermal forces and incomplete packing produce \u201cbreathing\u201d motions that allow internal rearrangement. Packing dynamics therefore inform protein allostery, conformational change, and folding. While Voronoi tessellation is a promising approach to this end, its application to proteins has been mainly focused on static structures. Here, the Voro++ library is adopted to investigate time\u2010dependent amino acid packing in molecular dynamics trajectories of a titin immunoglobulin domain at 300 and 400\u2009K. Tracking per\u2010residue Voronoi volume changes and reorganization of neighbor faces in the Voronoi lattice reveals residue\u2010level volume shifts and the corresponding timing of localized protein swelling. Side\u2010chain motion into and out of the protein core can also be monitored by mapping neighbor switching. This framework is applicable to detecting delicate changes preceding protein conformational transition or unfolding, and analyzing protein\u2013protein interface reorganization or surface hydration.<\/jats:p>","DOI":"10.1002\/jcc.70499","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T05:59:20Z","timestamp":1790056760000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Time\u2010Dependent Voronoi Analysis of Amino Acid Side\u2010Chain Packing in Simulations"],"prefix":"10.1002","volume":"47","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-5663-8734","authenticated-orcid":false,"given":"Sofiya B.","family":"Bettencourt","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering Texas A&amp;M University  College Station Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7514-3186","authenticated-orcid":false,"given":"Wonmuk","family":"Hwang","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering Texas A&amp;M University  College Station Texas USA"},{"name":"Department of Materials Science &amp; Engineering Texas A&amp;M University  College Station Texas USA"},{"name":"Department of Physics &amp; Astronomy Texas A&amp;M University  College Station Texas USA"},{"name":"Center for AI and Natural Sciences Korea Institute for Advanced Study  Seoul Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,21]]},"reference":[{"key":"e_1_2_9_2_1","first-page":"440","volume-title":"Methods in Enzymology","author":"Richards F. 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