{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T11:26:31Z","timestamp":1774524391705,"version":"3.50.1"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2017,5,3]],"date-time":"2017-05-03T00:00:00Z","timestamp":1493769600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,7,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>DynOmics (dynomics.pitt.edu) is a portal developed to leverage rapidly growing structural proteomics data by efficiently and accurately evaluating the dynamics of structurally resolved systems, from individual molecules to large complexes and assemblies, in the context of their physiological environment. At the core of the portal is a newly developed server, ENM 1.0, which permits users to efficiently generate information on the collective dynamics of any structure in PDB format, user-uploaded or database-retrieved. ENM 1.0 integrates two widely used elastic network models (ENMs)\u2014the Gaussian Network Model (GNM) and the Anisotropic Network Model (ANM), extended to take account of molecular environment. It enables users to assess potentially functional sites, signal transduction or allosteric communication mechanisms, and protein\u2013protein and protein\u2013DNA interaction poses, in addition to delivering ensembles of accessible conformers reconstructed at atomic details based on the global modes of motions predicted by the ANM. The \u2018environment\u2019 is defined in a flexible manner, from lipid bilayer and crystal contacts, to substrate or ligands bound to a protein, or surrounding subunits in a multimeric structure or assembly. User-friendly interactive features permit users to easily visualize how the environment alter the intrinsic dynamics of the query systems. ENM 1.0 can be accessed at http:\/\/enm.pitt.edu\/ or http:\/\/dyn.life.nthu.edu.tw\/oENM\/.<\/jats:p>","DOI":"10.1093\/nar\/gkx385","type":"journal-article","created":{"date-parts":[[2017,4,25]],"date-time":"2017-04-25T19:09:39Z","timestamp":1493147379000},"page":"W374-W380","source":"Crossref","is-referenced-by-count":144,"title":["DynOmics: dynamics of structural proteome and beyond"],"prefix":"10.1093","volume":"45","author":[{"given":"Hongchun","family":"Li","sequence":"first","affiliation":[{"name":"Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh PA, 15213, USA"}]},{"given":"Yuan-Yu","family":"Chang","sequence":"first","affiliation":[{"name":"Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Taiwan"}]},{"given":"Ji Young","family":"Lee","sequence":"first","affiliation":[{"name":"Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh PA, 15213, USA"}]},{"given":"Ivet","family":"Bahar","sequence":"first","affiliation":[{"name":"Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh PA, 15213, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3971-6386","authenticated-orcid":false,"given":"Lee-Wei","family":"Yang","sequence":"first","affiliation":[{"name":"Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Taiwan"}]}],"member":"286","published-online":{"date-parts":[[2017,5,3]]},"reference":[{"key":"2020041422553829400_B1","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.sbi.2015.07.007","article-title":"Adaptability of protein structures to enable functional interactions and evolutionary implications","volume":"35","author":"Haliloglu","year":"2015","journal-title":"Curr. 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