cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA
Abstract The sequence-dependent statistical mechanical properties of fragments of double-stranded DNA is believed to be pertinent to its biological function at length scales from a few base pairs (or bp) to a few hundreds of bp, e.g. indirect read-out protein binding sites, nucleosome positioning se...
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| Veröffentlicht in: | Nucleic acids research 2018-07, Vol.46 (W1), p.W5-W10 |
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| creator | De Bruin, Lennart Maddocks, John H |
| description | Abstract
The sequence-dependent statistical mechanical properties of fragments of double-stranded DNA is believed to be pertinent to its biological function at length scales from a few base pairs (or bp) to a few hundreds of bp, e.g. indirect read-out protein binding sites, nucleosome positioning sequences, phased A-tracts, etc. In turn, the equilibrium statistical mechanics behaviour of DNA depends upon its ground state configuration, or minimum free energy shape, as well as on its fluctuations as governed by its stiffness (in an appropriate sense). We here present cgDNAweb, which provides browser-based interactive visualization of the sequence-dependent ground states of double-stranded DNA molecules, as predicted by the underlying cgDNA coarse-grain rigid-base model of fragments with arbitrary sequence. The cgDNAweb interface is specifically designed to facilitate comparison between ground state shapes of different sequences. The server is freely available at cgDNAweb.epfl.ch with no login requirement. |
| doi_str_mv | 10.1093/nar/gky351 |
| format | Article |
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The sequence-dependent statistical mechanical properties of fragments of double-stranded DNA is believed to be pertinent to its biological function at length scales from a few base pairs (or bp) to a few hundreds of bp, e.g. indirect read-out protein binding sites, nucleosome positioning sequences, phased A-tracts, etc. In turn, the equilibrium statistical mechanics behaviour of DNA depends upon its ground state configuration, or minimum free energy shape, as well as on its fluctuations as governed by its stiffness (in an appropriate sense). We here present cgDNAweb, which provides browser-based interactive visualization of the sequence-dependent ground states of double-stranded DNA molecules, as predicted by the underlying cgDNA coarse-grain rigid-base model of fragments with arbitrary sequence. The cgDNAweb interface is specifically designed to facilitate comparison between ground state shapes of different sequences. The server is freely available at cgDNAweb.epfl.ch with no login requirement.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gky351</identifier><identifier>PMID: 29905876</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Chromatin Assembly and Disassembly - genetics ; Computational Biology - instrumentation ; DNA - chemistry ; DNA - genetics ; Internet ; Models, Molecular ; Nucleic Acid Conformation ; Nucleosomes - chemistry ; Nucleosomes - genetics ; Proteins - chemistry ; Proteins - genetics ; Software ; Web Server Issue</subject><ispartof>Nucleic acids research, 2018-07, Vol.46 (W1), p.W5-W10</ispartof><rights>The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. 2018</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c408t-2b6e921d910cbb09612fd1093b291c8bc5784df06431d0228f61076f41fdbefe3</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030996/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030996/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,1604,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29905876$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>De Bruin, Lennart</creatorcontrib><creatorcontrib>Maddocks, John H</creatorcontrib><title>cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
The sequence-dependent statistical mechanical properties of fragments of double-stranded DNA is believed to be pertinent to its biological function at length scales from a few base pairs (or bp) to a few hundreds of bp, e.g. indirect read-out protein binding sites, nucleosome positioning sequences, phased A-tracts, etc. In turn, the equilibrium statistical mechanics behaviour of DNA depends upon its ground state configuration, or minimum free energy shape, as well as on its fluctuations as governed by its stiffness (in an appropriate sense). We here present cgDNAweb, which provides browser-based interactive visualization of the sequence-dependent ground states of double-stranded DNA molecules, as predicted by the underlying cgDNA coarse-grain rigid-base model of fragments with arbitrary sequence. The cgDNAweb interface is specifically designed to facilitate comparison between ground state shapes of different sequences. The server is freely available at cgDNAweb.epfl.ch with no login requirement.</description><subject>Chromatin Assembly and Disassembly - genetics</subject><subject>Computational Biology - instrumentation</subject><subject>DNA - chemistry</subject><subject>DNA - genetics</subject><subject>Internet</subject><subject>Models, Molecular</subject><subject>Nucleic Acid Conformation</subject><subject>Nucleosomes - chemistry</subject><subject>Nucleosomes - genetics</subject><subject>Proteins - chemistry</subject><subject>Proteins - genetics</subject><subject>Software</subject><subject>Web Server Issue</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kU1PGzEQhi1UBCH00h-AfKmEkLYZe3edNQekKPQDCcGFni1_jMPSzTq1d4vy7zENReXCaQ7zzDvvzEvIJwZfGMhy1us4W_3aljXbIxNWCl5UUvAPZAIl1AWDqjkkRyk9ALCK1dUBOeRSQt3MxYRYu7q8WTyiOaea5kLbfsDotUU6BDrcI_0L0IS_R-wtFg432DvsB2qDjgmLVdRtT9fBYUeDpy6MpsMiDVFnzNE8fEz2ve4SfnypU_Lz29e75Y_i-vb71XJxXdgKmqHgRqDkzEkG1hiQgnHvng80XDLbGFvPm8p5EFXJHHDeeMFgLnzFvDPosZySi53uZjRrdDabjLpTm9iuddyqoFv1ttO392oV_iiRHyWlyAKnLwIx5HPToNZtsth1uscwJsWhFqWEvDujZzvUxpBSRP-6hoF6Nq1yKmqXSoZP_jf2iv6LIQOfd0AYN-8JPQGACJZE</recordid><startdate>20180702</startdate><enddate>20180702</enddate><creator>De Bruin, Lennart</creator><creator>Maddocks, John H</creator><general>Oxford University Press</general><scope>TOX</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20180702</creationdate><title>cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA</title><author>De Bruin, Lennart ; Maddocks, John H</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c408t-2b6e921d910cbb09612fd1093b291c8bc5784df06431d0228f61076f41fdbefe3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Chromatin Assembly and Disassembly - genetics</topic><topic>Computational Biology - instrumentation</topic><topic>DNA - chemistry</topic><topic>DNA - genetics</topic><topic>Internet</topic><topic>Models, Molecular</topic><topic>Nucleic Acid Conformation</topic><topic>Nucleosomes - chemistry</topic><topic>Nucleosomes - genetics</topic><topic>Proteins - chemistry</topic><topic>Proteins - genetics</topic><topic>Software</topic><topic>Web Server Issue</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>De Bruin, Lennart</creatorcontrib><creatorcontrib>Maddocks, John H</creatorcontrib><collection>Oxford Journals Open Access Collection</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>De Bruin, Lennart</au><au>Maddocks, John H</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2018-07-02</date><risdate>2018</risdate><volume>46</volume><issue>W1</issue><spage>W5</spage><epage>W10</epage><pages>W5-W10</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Abstract
The sequence-dependent statistical mechanical properties of fragments of double-stranded DNA is believed to be pertinent to its biological function at length scales from a few base pairs (or bp) to a few hundreds of bp, e.g. indirect read-out protein binding sites, nucleosome positioning sequences, phased A-tracts, etc. In turn, the equilibrium statistical mechanics behaviour of DNA depends upon its ground state configuration, or minimum free energy shape, as well as on its fluctuations as governed by its stiffness (in an appropriate sense). We here present cgDNAweb, which provides browser-based interactive visualization of the sequence-dependent ground states of double-stranded DNA molecules, as predicted by the underlying cgDNA coarse-grain rigid-base model of fragments with arbitrary sequence. The cgDNAweb interface is specifically designed to facilitate comparison between ground state shapes of different sequences. The server is freely available at cgDNAweb.epfl.ch with no login requirement.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>29905876</pmid><doi>10.1093/nar/gky351</doi><oa>free_for_read</oa></addata></record> |
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| ispartof | Nucleic acids research, 2018-07, Vol.46 (W1), p.W5-W10 |
| issn | 0305-1048 1362-4962 |
| language | eng |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; Oxford Journals Open Access Collection; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Chromatin Assembly and Disassembly - genetics Computational Biology - instrumentation DNA - chemistry DNA - genetics Internet Models, Molecular Nucleic Acid Conformation Nucleosomes - chemistry Nucleosomes - genetics Proteins - chemistry Proteins - genetics Software Web Server Issue |
| title | cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA |
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