A grid-enabled web service for low-resolution crystal structure refinement
Identifieur interne : 000445 ( Pmc/Checkpoint ); précédent : 000444; suivant : 000446A grid-enabled web service for low-resolution crystal structure refinement
Auteurs : Daniel J. O Onovan [États-Unis] ; Ian Stokes-Rees [États-Unis] ; Yunsun Nam [États-Unis] ; Stephen C. Blacklow [États-Unis] ; Gunnar F. Schröder [Allemagne] ; Axel T. Brunger [États-Unis] ; Piotr Sliz [États-Unis]Source :
- Acta Crystallographica Section D: Biological Crystallography [ 0907-4449 ] ; 2012.
Abstract
The deformable elastic network (DEN) method for reciprocal-space crystallographic refinement improves crystal structures, especially at resolutions lower than 3.5 Å. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements.
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DOI: 10.1107/S0907444912001163
PubMed: 22349228
PubMed Central: 3282622
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O Onovan</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Stokes Rees, Ian" sort="Stokes Rees, Ian" uniqKey="Stokes Rees I" first="Ian" last="Stokes-Rees">Ian Stokes-Rees</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Nam, Yunsun" sort="Nam, Yunsun" uniqKey="Nam Y" first="Yunsun" last="Nam">Yunsun Nam</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Blacklow, Stephen C" sort="Blacklow, Stephen C" uniqKey="Blacklow S" first="Stephen C." last="Blacklow">Stephen C. Blacklow</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="b">Department of Cancer Biology,<institution>Dana Farber Cancer Institute</institution>, Boston, MA 02215,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="c">Department of Pathology,<institution>Brigham and Women’s Hospital</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Schroder, Gunnar F" sort="Schroder, Gunnar F" uniqKey="Schroder G" first="Gunnar F." last="Schröder">Gunnar F. Schröder</name><affiliation wicri:level="1"><nlm:aff id="d">Forschungszentrum Jülich,<institution>Institute of Complex Systems (ICS-6)</institution>, 52425 Jülich,<country>Germany</country></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Brunger, Axel T" sort="Brunger, Axel T" uniqKey="Brunger A" first="Axel T." last="Brunger">Axel T. Brunger</name><affiliation wicri:level="1"><nlm:aff id="e">Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science,<institution>Stanford School of Medicine</institution>, J. H. 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O Onovan</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Stokes Rees, Ian" sort="Stokes Rees, Ian" uniqKey="Stokes Rees I" first="Ian" last="Stokes-Rees">Ian Stokes-Rees</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Nam, Yunsun" sort="Nam, Yunsun" uniqKey="Nam Y" first="Yunsun" last="Nam">Yunsun Nam</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Blacklow, Stephen C" sort="Blacklow, Stephen C" uniqKey="Blacklow S" first="Stephen C." last="Blacklow">Stephen C. Blacklow</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="b">Department of Cancer Biology,<institution>Dana Farber Cancer Institute</institution>, Boston, MA 02215,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="c">Department of Pathology,<institution>Brigham and Women’s Hospital</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Schroder, Gunnar F" sort="Schroder, Gunnar F" uniqKey="Schroder G" first="Gunnar F." last="Schröder">Gunnar F. Schröder</name><affiliation wicri:level="1"><nlm:aff id="d">Forschungszentrum Jülich,<institution>Institute of Complex Systems (ICS-6)</institution>, 52425 Jülich,<country>Germany</country></nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Brunger, Axel T" sort="Brunger, Axel T" uniqKey="Brunger A" first="Axel T." last="Brunger">Axel T. Brunger</name><affiliation wicri:level="1"><nlm:aff id="e">Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science,<institution>Stanford School of Medicine</institution>, J. H. Clark Center E300C, 318 Campus Drive, Stanford, CA 94305,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Sliz, Piotr" sort="Sliz, Piotr" uniqKey="Sliz P" first="Piotr" last="Sliz">Piotr Sliz</name><affiliation wicri:level="1"><nlm:aff id="a">Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="f">Laboratory of Molecular Medicine,<institution>Children’s Hospital</institution>, Boston, MA 02115,<country>USA</country></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Acta Crystallographica Section D: Biological Crystallography</title><idno type="ISSN">0907-4449</idno><idno type="eISSN">1399-0047</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The deformable elastic network (DEN) method for reciprocal-space crystallographic refinement improves crystal structures, especially at resolutions lower than 3.5 Å. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Acta Crystallogr D Biol Crystallogr</journal-id><journal-id journal-id-type="publisher-id">Acta Cryst. D</journal-id><journal-title-group><journal-title>Acta Crystallographica Section D: Biological Crystallography</journal-title></journal-title-group><issn pub-type="ppub">0907-4449</issn><issn pub-type="epub">1399-0047</issn><publisher><publisher-name>International Union of Crystallography</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22349228</article-id><article-id pub-id-type="pmc">3282622</article-id><article-id pub-id-type="publisher-id">dz5246</article-id><article-id pub-id-type="doi">10.1107/S0907444912001163</article-id><article-id pub-id-type="coden">ABCRE6</article-id><article-id pub-id-type="pii">S0907444912001163</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Papers</subject></subj-group></article-categories><title-group><article-title>A grid-enabled web service for low-resolution crystal structure refinement</article-title><alt-title>DEN web service</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>O’Donovan</surname><given-names>Daniel J.</given-names></name><xref ref-type="aff" rid="a">a</xref></contrib><contrib contrib-type="author"><name><surname>Stokes-Rees</surname><given-names>Ian</given-names></name><xref ref-type="aff" rid="a">a</xref></contrib><contrib contrib-type="author"><name><surname>Nam</surname><given-names>Yunsun</given-names></name><xref ref-type="aff" rid="a">a</xref></contrib><contrib contrib-type="author"><name><surname>Blacklow</surname><given-names>Stephen C.</given-names></name><xref ref-type="aff" rid="a">a</xref><xref ref-type="aff" rid="b">b</xref><xref ref-type="aff" rid="c">c</xref></contrib><contrib contrib-type="author"><name><surname>Schröder</surname><given-names>Gunnar F.</given-names></name><xref ref-type="aff" rid="d">d</xref></contrib><contrib contrib-type="author"><name><surname>Brunger</surname><given-names>Axel T.</given-names></name><xref ref-type="aff" rid="e">e</xref></contrib><contrib contrib-type="author"><name><surname>Sliz</surname><given-names>Piotr</given-names></name><xref ref-type="aff" rid="a">a</xref><xref ref-type="aff" rid="f">f</xref><xref ref-type="corresp" rid="cor">*</xref></contrib><aff id="a"><label>a</label>Department of Biological Chemistry and Molecular Pharmacology,<institution>Harvard Medical School</institution>, Boston, MA 02115,<country>USA</country></aff><aff id="b"><label>b</label>Department of Cancer Biology,<institution>Dana Farber Cancer Institute</institution>, Boston, MA 02215,<country>USA</country></aff><aff id="c"><label>c</label>Department of Pathology,<institution>Brigham and Women’s Hospital</institution>, Boston, MA 02115,<country>USA</country></aff><aff id="d"><label>d</label>Forschungszentrum Jülich,<institution>Institute of Complex Systems (ICS-6)</institution>, 52425 Jülich,<country>Germany</country></aff><aff id="e"><label>e</label>Howard Hughes Medical Institute and Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science,<institution>Stanford School of Medicine</institution>, J. H. Clark Center E300C, 318 Campus Drive, Stanford, CA 94305,<country>USA</country></aff><aff id="f"><label>f</label>Laboratory of Molecular Medicine,<institution>Children’s Hospital</institution>, Boston, MA 02115,<country>USA</country></aff></contrib-group><author-notes><corresp id="cor">Correspondence e-mail: <email>sliz@hkl.hms.harvard.edu</email></corresp></author-notes><pub-date pub-type="ppub"><day>01</day><month>3</month><year>2012</year></pub-date><pub-date pub-type="epub"><day>14</day><month>2</month><year>2012</year></pub-date><pub-date pub-type="pmc-release"><day>14</day><month>2</month><year>2012</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>68</volume><issue>Pt 3</issue><issue-id pub-id-type="publisher-id">d120300</issue-id><fpage>261</fpage><lpage>267</lpage><history><date date-type="received"><day>09</day><month>11</month><year>2011</year></date><date date-type="accepted"><day>10</day><month>1</month><year>2012</year></date></history><permissions><copyright-statement>© O'Donovan et al. 2012</copyright-statement><copyright-year>2012</copyright-year><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0/uk/"><license-p>This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.</license-p></license></permissions><self-uri xlink:type="simple" xlink:href="http://dx.doi.org/10.1107/S0907444912001163">A full version of this article is available from Crystallography Journals Online.</self-uri><abstract abstract-type="toc"><p>The deformable elastic network (DEN) method for reciprocal-space crystallographic refinement improves crystal structures, especially at resolutions lower than 3.5 Å. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements.</p></abstract><abstract><p>Deformable elastic network (DEN) restraints have proved to be a powerful tool for refining structures from low-resolution X-ray crystallographic data sets. Unfortunately, optimal refinement using DEN restraints requires extensive calculations and is often hindered by a lack of access to sufficient computational resources. The DEN web service presented here intends to provide structural biologists with access to resources for running computationally intensive DEN refinements in parallel on the Open Science Grid, the US cyberinfrastructure. Access to the grid is provided through a simple and intuitive web interface integrated into the SBGrid Science Portal. Using this portal, refinements combined with full parameter optimization that would take many thousands of hours on standard computational resources can now be completed in several hours. An example of the successful application of DEN restraints to the human Notch1 transcriptional complex using the grid resource, and summaries of all submitted refinements, are presented as justification.</p></abstract><kwd-group><kwd>deformable elastic network restraints</kwd><kwd>low-resolution refinement</kwd><kwd>DEN refinement</kwd></kwd-group></article-meta></front><floats-group><fig id="fig1" position="float"><label>Figure 1</label><caption><p>Heat map showing how (X-ray-determined) Protein Data Bank (PDB) entries trend with data resolution and molecular weight. There are many structures recorded between 1.5 and 2.5 Å resolution with a molecular weight of around 40 kDa, indicated by a lighter color. The white dots represent the mean average resolutions for structures in 10 kDa ranges. This figure shows that larger molecules tend to have poorer resolutions. As the molecular weight of structures increases, the mean resolution of the recorded X-ray data also increases. The PDB only contains structures that have been finalized; therefore, there may be many more low-resolution data sets from crystals that did not yield publication-quality structures.</p></caption><graphic xlink:href="d-68-00261-fig1"></graphic></fig><fig id="fig2" position="float"><label>Figure 2</label><caption><p>DEN Portal Application job-submission interface. This is the form through which registered users can submit new tasks to the Open Science Grid. The form requires a unique ‘task name’, DEN input file, data archive and the resolution of the diffraction data for <italic>PROCHECK</italic> validity checking. There are other optional parameters.</p></caption><graphic xlink:href="d-68-00261-fig2"></graphic></fig><fig id="fig3" position="float"><label>Figure 3</label><caption><p>Test case: a Notch1 transcription complex containing the RAM region. (<italic>a</italic>) The first 4.2–7 Å low-resolution structure of a human Notch1 complex consisting of the Notch ankyrin-repeat domain, the CSL transcription factor and the Mastermind-like 1 (MAML-1) co-activator was determined by combining molecular replacement and selenomethionine scanning. Single Leu-to-Met or Val-to-Met mutations (labeled with the MAML-1 residue number) were introduced into the MAML-1 polypeptide for incorporation of selenomethionine. Anomalous Fourier difference maps were calculated for each of five mutants (the high-resolution limit for each data set was between 6 and 7.5 Å) using the anomalous signal from selenomethionine and the phase calculated by molecular replacement. Each map shows a clear peak at the predicted location of the mutated residue, indicated by the matching colors. The gray mesh represents the density for the MAML-1 as part of a 2<italic>F</italic><sub>o</sub> − <italic>F</italic><sub>c</sub> density map calculated without any atoms modeled for the MAML-1 helix. Adapted from the supplementary information in Nam <italic>et al.</italic> (2006<xref ref-type="bibr" rid="bb10"> ▶</xref>). (<italic>b</italic>) An <italic>R</italic><sub>free</sub> heat map of results from the Notch protein DEN optimization using an initial starting temperature of 1000 K. The minimal <italic>R</italic><sub>free</sub> values for each parameter pair (ω<sub>DEN</sub> and γ<sub>DEN</sub>) over multiple refinement repeats are shown. (<italic>c</italic>) The corresponding Ramachandran statistics (percentage of disallowed backbone angles). For each parameter pair, the structure with the lowest <italic>R</italic><sub>free</sub> value was usen to calculate the Ramachandran statistics. (<italic>d</italic>) A histogram showing all calculated <italic>R</italic><sub>free</sub> for a complete portal DEN optimization of the Notch1 complex. The dashed line is the best that could be achieved without DEN (<italic>i.e.</italic>, the lowest <italic>R</italic><sub>free</sub> of the all the ‘no DEN’ repeat refinements); the lowest (or best) <italic>R</italic><sub>free</sub> chosen is the far left tail of the histogram.</p></caption><graphic xlink:href="d-68-00261-fig3"></graphic></fig><fig id="fig4" position="float"><label>Figure 4</label><caption><p>Chart showing <italic>R</italic><sub>free</sub> (optimum over all results) and <italic>R</italic><sub>free</sub> (no DEN; optimum over all control refinements without DEN) for all tasks submitted by users. Each point lies below the diagonal line, showing that all results demonstrated an improvement in <italic>R</italic><sub>free</sub> over the control results.</p></caption><graphic xlink:href="d-68-00261-fig4"></graphic></fig></floats-group></pmc><affiliations><list><country><li>Allemagne</li><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="O Onovan, Daniel J" sort="O Onovan, Daniel J" uniqKey="O Onovan D" first="Daniel J." last="O Onovan">Daniel J. O Onovan</name></noRegion><name sortKey="Blacklow, Stephen C" sort="Blacklow, Stephen C" uniqKey="Blacklow S" first="Stephen C." last="Blacklow">Stephen C. Blacklow</name><name sortKey="Blacklow, Stephen C" sort="Blacklow, Stephen C" uniqKey="Blacklow S" first="Stephen C." last="Blacklow">Stephen C. Blacklow</name><name sortKey="Blacklow, Stephen C" sort="Blacklow, Stephen C" uniqKey="Blacklow S" first="Stephen C." last="Blacklow">Stephen C. Blacklow</name><name sortKey="Brunger, Axel T" sort="Brunger, Axel T" uniqKey="Brunger A" first="Axel T." last="Brunger">Axel T. Brunger</name><name sortKey="Nam, Yunsun" sort="Nam, Yunsun" uniqKey="Nam Y" first="Yunsun" last="Nam">Yunsun Nam</name><name sortKey="Sliz, Piotr" sort="Sliz, Piotr" uniqKey="Sliz P" first="Piotr" last="Sliz">Piotr Sliz</name><name sortKey="Sliz, Piotr" sort="Sliz, Piotr" uniqKey="Sliz P" first="Piotr" last="Sliz">Piotr Sliz</name><name sortKey="Stokes Rees, Ian" sort="Stokes Rees, Ian" uniqKey="Stokes Rees I" first="Ian" last="Stokes-Rees">Ian Stokes-Rees</name></country><country name="Allemagne"><noRegion><name sortKey="Schroder, Gunnar F" sort="Schroder, Gunnar F" uniqKey="Schroder G" first="Gunnar F." last="Schröder">Gunnar F. Schröder</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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