{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T13:00:29Z","timestamp":1761742829135},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"21","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We built a novel web-based platform for performing discrete molecular dynamics simulations of proteins. In silico protein folding involves searching for minimal frustration in the vast conformational landscape. Conventional approaches for simulating protein folding insufficiently address the problem of simulations in relevant time and length scales necessary for a mechanistic understanding of underlying biomolecular phenomena. Discrete molecular dynamics (DMD) offers an opportunity to bridge the size and timescale gaps and uncover the structural and biological properties of experimentally undetectable protein dynamics. The iFold server supports large-scale simulations of protein folding, thermal denaturation, thermodynamic scan, simulated annealing and pfold analysis using DMD and coarse-grained protein model with structure-based G\u014d-interactions between amino acids.<\/jats:p>\n               <jats:p>Availability: \u00a0<\/jats:p>\n               <jats:p>Contact: \u00a0dokh@med.unc.edu<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl460","type":"journal-article","created":{"date-parts":[[2006,8,30]],"date-time":"2006-08-30T08:21:24Z","timestamp":1156926084000},"page":"2693-2694","source":"Crossref","is-referenced-by-count":20,"title":["iFold: a platform for interactive folding simulations of proteins"],"prefix":"10.1093","volume":"22","author":[{"given":"Shantanu","family":"Sharma","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Biophysics, University of North Carolina 1 \u00a0 1 \u00a0 \u00a0 Chapel Hill, NC 27599, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feng","family":"Ding","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics, University of North Carolina 1 \u00a0 1 \u00a0 \u00a0 Chapel Hill, NC 27599, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huifen","family":"Nie","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics, University of North Carolina 1 \u00a0 1 \u00a0 \u00a0 Chapel Hill, NC 27599, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniel","family":"Watson","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of North Carolina 2 \u00a0 2 \u00a0 \u00a0 Chapel Hill, NC 27599, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aditya","family":"Unnithan","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of North Carolina 2 \u00a0 2 \u00a0 \u00a0 Chapel Hill, NC 27599, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jameson","family":"Lopp","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of North Carolina 2 \u00a0 2 \u00a0 \u00a0 Chapel Hill, NC 27599, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Diane","family":"Pozefsky","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of North Carolina 2 \u00a0 2 \u00a0 \u00a0 Chapel Hill, NC 27599, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nikolay V.","family":"Dokholyan","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics, University of North Carolina 1 \u00a0 1 \u00a0 \u00a0 Chapel Hill, NC 27599, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,8,29]]},"reference":[{"key":"2023012408431470500_b1","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1016\/j.tibtech.2005.07.001","article-title":"Simple but predictive protein models","volume":"23","author":"Ding","year":"2005","journal-title":"Trends Biotechnol."},{"key":"2023012408431470500_b2","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1016\/j.str.2005.04.009","article-title":"Scaling behavior and structure of denatured proteins","volume":"13","author":"Ding","year":"2005","journal-title":"Structure"},{"key":"2023012408431470500_b3","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/S1359-0278(98)00072-8","article-title":"Discrete molecular dynamics studies of the folding of a protein-like model","volume":"3","author":"Dokholyan","year":"1998","journal-title":"Fold Des."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/21\/2693\/48839278\/bioinformatics_22_21_2693.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/21\/2693\/48839278\/bioinformatics_22_21_2693.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T09:05:18Z","timestamp":1674551118000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/21\/2693\/252379"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,8,29]]},"references-count":3,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2006,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl460","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,11,1]]},"published":{"date-parts":[[2006,8,29]]}}}