{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,4,6]],"date-time":"2023-04-06T01:44:48Z","timestamp":1680745488755},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: We present the \u2018Dynamic Packing Grid\u2019 (DPG), a neighborhood data structure for maintaining and manipulating flexible molecules and assemblies, for efficient computation of binding affinities in drug design or in molecular dynamics calculations.<\/jats:p>\n               <jats:p>Results: \u00a0DPG can efficiently maintain the molecular surface using only linear space and supports quasi-constant time insertion, deletion and movement (i.e. updates) of atoms or groups of atoms. DPG also supports constant time neighborhood queries from arbitrary points. Our results for maintenance of molecular surface and polarization energy computations using DPG exhibit marked improvement in time and space requirements.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/www.cs.utexas.edu\/~bajaj\/cvc\/software\/DPG.shtml<\/jats:p>\n               <jats:p>Contact: \u00a0bajaj@cs.utexas.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq627","type":"journal-article","created":{"date-parts":[[2010,11,27]],"date-time":"2010-11-27T01:19:15Z","timestamp":1290820755000},"page":"55-62","source":"Crossref","is-referenced-by-count":8,"title":["A dynamic data structure for flexible molecular maintenance and informatics"],"prefix":"10.1093","volume":"27","author":[{"given":"Chandrajit","family":"Bajaj","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Texas at Austin, Austin, TX, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rezaul Alam","family":"Chowdhury","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Texas at Austin, Austin, TX, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Muhibur","family":"Rasheed","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Texas at Austin, Austin, TX, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,11,25]]},"reference":[{"key":"2023012511160281300_B1","doi-asserted-by":"crossref","first-page":"4524","DOI":"10.1137\/090746173","article-title":"Fast molecular solvation energetics and force computation","volume":"31","author":"Bajaj","year":"2010","journal-title":"SIAM J. 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