Using Sculptor and Situs for Simultaneous Assembly of Atomic Components into Low-Resolution Shapes
Identifieur interne : 001041 ( Pmc/Curation ); précédent : 001040; suivant : 001042Using Sculptor and Situs for Simultaneous Assembly of Atomic Components into Low-Resolution Shapes
Auteurs : Stefan Birmanns [États-Unis] ; Mirabela Rusu [États-Unis] ; Willy Wriggers [États-Unis]Source :
- Journal of Structural Biology [ 1047-8477 ] ; 2010.
Abstract
We describe an integrated software system called
Url:
DOI: 10.1016/j.jsb.2010.11.002
PubMed: 21078392
PubMed Central: 3352678
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and <italic>Situs</italic>
for Simultaneous Assembly of Atomic Components into Low-Resolution Shapes</title>
<author><name sortKey="Birmanns, Stefan" sort="Birmanns, Stefan" uniqKey="Birmanns S" first="Stefan" last="Birmanns">Stefan Birmanns</name>
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<front><div type="abstract" xml:lang="en"><p id="P2">We describe an integrated software system called <italic>Sculptor</italic>
that combines visualization capabilities with molecular modeling algorithms for the analysis of multi-scale data sets. <italic>Sculptor</italic>
features extensive special purpose visualization techniques that are based on modern GPU programming and are capable of representing complex molecular assemblies in real-time. The integration of graphics and modeling offers several advantages. The user interface not only eases the usually steep learning curve of pure algorithmic techniques, but it also permits instant analysis and post-processing of results, as well as the integration of results from external software. Here, we implemented an interactive peak-selection strategy that enables the user to explore a preliminary score landscape generated by the <italic>colores</italic>
tool of <italic>Situs</italic>
. The interactive placement of components, one at a time, is advantageous for low-resolution or ambiguously shaped maps, which are sometimes difficult to interpret by the fully automatic peak selection of <italic>colores</italic>
. For the subsequent refinement of the preliminary models resulting from both interactive and automatic peak selection, we have implemented a novel simultaneous multi-body docking in <italic>Sculptor</italic>
and <italic>Situs</italic>
that softly enforces shape complementarities between components using the normalization of the cross-correlation coefficient. The proposed techniques are freely available in <italic>Situs</italic>
version 2.6 and <italic>Sculptor</italic>
version 2.0.</p>
</div>
</front>
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<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">9011206</journal-id>
<journal-id journal-id-type="pubmed-jr-id">1746</journal-id>
<journal-id journal-id-type="nlm-ta">J Struct Biol</journal-id>
<journal-title>Journal of Structural Biology</journal-title>
<issn pub-type="ppub">1047-8477</issn>
<issn pub-type="epub">1095-8657</issn>
</journal-meta>
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<article-id pub-id-type="doi">10.1016/j.jsb.2010.11.002</article-id>
<article-id pub-id-type="manuscript">NIHMS262945</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Using <italic>Sculptor</italic>
and <italic>Situs</italic>
for Simultaneous Assembly of Atomic Components into Low-Resolution Shapes</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Birmanns</surname>
<given-names>Stefan</given-names>
</name>
<xref rid="A1" ref-type="aff">a</xref>
<xref rid="FN1" ref-type="author-notes">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rusu</surname>
<given-names>Mirabela</given-names>
</name>
<xref rid="A1" ref-type="aff">a</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wriggers</surname>
<given-names>Willy</given-names>
</name>
<xref rid="A1" ref-type="aff">a</xref>
<xref rid="FN2" ref-type="author-notes">1</xref>
</contrib>
</contrib-group>
<aff id="A1"><label>a</label>
University of Texas School of Biomedical Informatics at Houston, 7000 Fannin St. UCT 600, Houston TX 77030</aff>
<author-notes><corresp id="FN1"><label>*</label>
Corresponding author. Fax: +1 713 500 3907, <email>Stefan.Birmanns@uth.tmc.edu</email>
(Stefan Birmanns)</corresp>
<fn id="FN2" fn-type="present-address"><label>1</label>
<p>Present address: D.E. Shaw Research, 120 E. 45th St., New York, NY 10036, USA</p>
</fn>
</author-notes>
<pub-date pub-type="nihms-submitted"><day>28</day>
<month>1</month>
<year>2011</year>
</pub-date>
<pub-date pub-type="epub"><day>13</day>
<month>11</month>
<year>2010</year>
</pub-date>
<pub-date pub-type="ppub"><month>3</month>
<year>2011</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>15</day>
<month>5</month>
<year>2012</year>
</pub-date>
<volume>173</volume>
<issue>3</issue>
<fpage>428</fpage>
<lpage>435</lpage>
<abstract><p id="P2">We describe an integrated software system called <italic>Sculptor</italic>
that combines visualization capabilities with molecular modeling algorithms for the analysis of multi-scale data sets. <italic>Sculptor</italic>
features extensive special purpose visualization techniques that are based on modern GPU programming and are capable of representing complex molecular assemblies in real-time. The integration of graphics and modeling offers several advantages. The user interface not only eases the usually steep learning curve of pure algorithmic techniques, but it also permits instant analysis and post-processing of results, as well as the integration of results from external software. Here, we implemented an interactive peak-selection strategy that enables the user to explore a preliminary score landscape generated by the <italic>colores</italic>
tool of <italic>Situs</italic>
. The interactive placement of components, one at a time, is advantageous for low-resolution or ambiguously shaped maps, which are sometimes difficult to interpret by the fully automatic peak selection of <italic>colores</italic>
. For the subsequent refinement of the preliminary models resulting from both interactive and automatic peak selection, we have implemented a novel simultaneous multi-body docking in <italic>Sculptor</italic>
and <italic>Situs</italic>
that softly enforces shape complementarities between components using the normalization of the cross-correlation coefficient. The proposed techniques are freely available in <italic>Situs</italic>
version 2.6 and <italic>Sculptor</italic>
version 2.0.</p>
</abstract>
<kwd-group><kwd>multi-resolution modeling</kwd>
<kwd>multi-component registration</kwd>
<kwd>macromolecular assembly</kwd>
<kwd>cryo-electron microscopy</kwd>
<kwd>immersive visualization</kwd>
<kwd>haptic rendering</kwd>
</kwd-group>
<contract-num rid="GM1">R01 GM062968-09
||GM</contract-num>
<contract-sponsor id="GM1">National Institute of General Medical Sciences : NIGMS</contract-sponsor>
</article-meta>
</front>
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