Molecular-level simulation of Pandemic Influenza Glycoproteins
Identifieur interne : 000876 ( Pmc/Corpus ); précédent : 000875; suivant : 000877Molecular-level simulation of Pandemic Influenza Glycoproteins
Auteurs : Rommie E. Amaro ; Wilfred W. LiSource :
- Methods in Molecular Biology (Clifton, N.j.) [ 1064-3745 ] ; 2012.
Abstract
Computational simulation of pandemic diseases provides important insight into many disease features that may benefit public health. This is especially true for the influenza virus, a continuing global pandemic threat. Molecular or atomic-level investigation of influenza has predominantly focused on the two major virus glycoproteins, neuraminidase (NA) and hemagglutinin (HA). In this chapter, we walk the readers through major considerations for studying pandemic influenza glycoproteins, from choosing the most useful choice of system(s) to avoiding common pitfalls in experimental design and execution. While a brief discussion of several potential simulation and docking techniques is presented, we emphasize molecular dynamics (MD) and Brownian dynamics (BD) simulation techniques and molecular docking, within the context of biologically outstanding questions in influenza research.
Url:
DOI: 10.1007/978-1-61779-465-0_34
PubMed: 22183559
PubMed Central: 3352029
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PMC:3352029Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Molecular-level simulation of Pandemic Influenza Glycoproteins</title><author><name sortKey="Amaro, Rommie E" sort="Amaro, Rommie E" uniqKey="Amaro R" first="Rommie E." last="Amaro">Rommie E. Amaro</name><affiliation><nlm:aff id="A1">Departments of Pharmaceutical Sciences, Computer Science, and Chemistry, University of California, Irvine, Irvine, CA 92697, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A2">National Biomedical Computation Resource, University of California, San Diego, San Diego, CA 92093, USA</nlm:aff></affiliation></author><author><name sortKey="Li, Wilfred W" sort="Li, Wilfred W" uniqKey="Li W" first="Wilfred W." last="Li">Wilfred W. Li</name><affiliation><nlm:aff id="A2">National Biomedical Computation Resource, University of California, San Diego, San Diego, CA 92093, USA</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22183559</idno><idno type="pmc">3352029</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3352029</idno><idno type="RBID">PMC:3352029</idno><idno type="doi">10.1007/978-1-61779-465-0_34</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000876</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000876</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Molecular-level simulation of Pandemic Influenza Glycoproteins</title><author><name sortKey="Amaro, Rommie E" sort="Amaro, Rommie E" uniqKey="Amaro R" first="Rommie E." last="Amaro">Rommie E. Amaro</name><affiliation><nlm:aff id="A1">Departments of Pharmaceutical Sciences, Computer Science, and Chemistry, University of California, Irvine, Irvine, CA 92697, USA</nlm:aff></affiliation><affiliation><nlm:aff id="A2">National Biomedical Computation Resource, University of California, San Diego, San Diego, CA 92093, USA</nlm:aff></affiliation></author><author><name sortKey="Li, Wilfred W" sort="Li, Wilfred W" uniqKey="Li W" first="Wilfred W." last="Li">Wilfred W. Li</name><affiliation><nlm:aff id="A2">National Biomedical Computation Resource, University of California, San Diego, San Diego, CA 92093, USA</nlm:aff></affiliation></author></analytic><series><title level="j">Methods in Molecular Biology (Clifton, N.j.)</title><idno type="ISSN">1064-3745</idno><idno type="eISSN">1940-6029</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Summary</title><p id="P1">Computational simulation of pandemic diseases provides important insight into many disease features that may benefit public health. This is especially true for the influenza virus, a continuing global pandemic threat. Molecular or atomic-level investigation of influenza has predominantly focused on the two major virus glycoproteins, neuraminidase (NA) and hemagglutinin (HA). In this chapter, we walk the readers through major considerations for studying pandemic influenza glycoproteins, from choosing the most useful choice of system(s) to avoiding common pitfalls in experimental design and execution. While a brief discussion of several potential simulation and docking techniques is presented, we emphasize molecular dynamics (MD) and Brownian dynamics (BD) simulation techniques and molecular docking, within the context of biologically outstanding questions in influenza research.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">9214969</journal-id><journal-id journal-id-type="pubmed-jr-id">2488</journal-id><journal-id journal-id-type="nlm-ta">Methods Mol Biol</journal-id><journal-id journal-id-type="iso-abbrev">Methods Mol. Biol.</journal-id><journal-title-group><journal-title>Methods in Molecular Biology (Clifton, N.j.)</journal-title></journal-title-group><issn pub-type="ppub">1064-3745</issn><issn pub-type="epub">1940-6029</issn></journal-meta><article-meta><article-id pub-id-type="pmid">22183559</article-id><article-id pub-id-type="pmc">3352029</article-id><article-id pub-id-type="doi">10.1007/978-1-61779-465-0_34</article-id><article-id pub-id-type="manuscript">NIHMS357662</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Molecular-level simulation of Pandemic Influenza Glycoproteins</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Amaro</surname><given-names>Rommie E.</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A2">2</xref><xref ref-type="corresp" rid="cor1">*</xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Wilfred W.</given-names></name><xref ref-type="aff" rid="A2">2</xref></contrib></contrib-group><aff id="A1"><label>1</label>Departments of Pharmaceutical Sciences, Computer Science, and Chemistry, University of California, Irvine, Irvine, CA 92697, USA</aff><aff id="A2"><label>2</label>National Biomedical Computation Resource, University of California, San Diego, San Diego, CA 92093, USA</aff><author-notes><corresp id="cor1"><label>*</label>To whom correspondence should be addressed: Prof. Rommie E. Amaro, Departments of Pharmaceutical Sciences, Computer Science, and Chemistry, University of California, Irvine, 3134C Natural Sciences 1, Irvine, CA 92697-3958. <email>ramaro@uci.edu</email>, Phone: 949-824-2559</corresp></author-notes><pub-date pub-type="nihms-submitted"><day>3</day><month>5</month><year>2012</year></pub-date><pub-date pub-type="ppub"><year>2012</year></pub-date><pub-date pub-type="pmc-release"><day>15</day><month>5</month><year>2012</year></pub-date><volume>819</volume><fpage>575</fpage><lpage>594</lpage><abstract><title>Summary</title><p id="P1">Computational simulation of pandemic diseases provides important insight into many disease features that may benefit public health. This is especially true for the influenza virus, a continuing global pandemic threat. Molecular or atomic-level investigation of influenza has predominantly focused on the two major virus glycoproteins, neuraminidase (NA) and hemagglutinin (HA). In this chapter, we walk the readers through major considerations for studying pandemic influenza glycoproteins, from choosing the most useful choice of system(s) to avoiding common pitfalls in experimental design and execution. While a brief discussion of several potential simulation and docking techniques is presented, we emphasize molecular dynamics (MD) and Brownian dynamics (BD) simulation techniques and molecular docking, within the context of biologically outstanding questions in influenza research.</p></abstract><kwd-group><kwd>Pandemic diseases</kwd><kwd>computational biology</kwd><kwd>influenza</kwd><kwd>neuraminidase</kwd><kwd>hemagglutinin</kwd><kwd>molecular dynamics simulations</kwd><kwd>Brownian dynamics simulations</kwd><kwd>binding free energy estimates</kwd><kwd>docking</kwd><kwd>antiviral design</kwd></kwd-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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