wwPDB: Small Angle Scattering (SAS)

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href='/task/validation-task-forces' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Validation Task Forces</a></li> <li ><a href='/task/xray' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> X-Ray Validation</a></li> <li ><a href='/task/nmr' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> NMR Validation</a></li> <li ><a href='/task/em' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> EM Validation</a></li> <li class='active'><a href='/task/sas' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Small Angle Scattering (SAS)</a></li> <li ><a href='/task/mmcif' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> PDBx/mmCIF Working Group</a></li> <li ><a href='/task/hybrid' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Hybrid/Integrative Methods</a></li> <li ><a href='/task/ligand-validation-workshop' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> Ligand Validation Workshop</a></li> <li ><a href='/task/modelcif' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> ModelCIF Working Group</a></li> </ul> </div> <div class="col-md-9"> <div class="wwpdb-content">  <h1>Small Angle Scattering Task Force</h1> <p> Method-specific Validation Task Forces have been convened to collect recommendations and develop consensus on additional validation that should be performed, and to identify software applications to perform validation tasks. </p> <p> The first meeting of the Small Angle Scattering (SAS) Task Force was held July 12-13, 2012 at the Center for Integrative Proteomics Research at Rutgers University in Piscataway, NJ. </p> <p> Their report has now been published: </p> <p> "Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB Structure" Jill Trewhella, Wayne A. Hendrickson, Gerard J. Kleywegt, Andrej Sali, Mamoru Sato, Torsten Schwede, Dmitri I. Svergun, John A. Tainer, John Westbrook and Helen M. Berman (2013) <i>Structure</i> 21: 875-881 [ doi:<a href="http://www.cell.com/structure/abstract/S0969-2126(13)00150-0" target="_blank">10.1016/j.str.2013.04.020</a> ] </p> <p> <a class="fancybox" rel="group" href="https://cdn.rcsb.org/wwpdb/img/task/sas_task_force.jpg"> <img class="img-responsive img-thumbnail" src="https://cdn.rcsb.org/wwpdb/img/task/sas_task_force_s.jpg" alt="SAS Task Force 2012 at Rutgers University" /> </a> <br/><caption>SAS Task Force 2012 at Rutgers University</caption> </p> <br /> <p> A second meeting was held May 12-14, 2014 at Rutgers. Participants included Jill Trewhella (Chair, University of Sydney), Torsten Schwede (University of Basel), Shuji Akiyama (Research Center of Integrative Molecular Systems (CIMoS), Japan), Dmitri Svergun (EMBL-Hamburg), Wayne Hendrickson (Columbia University), John A. Tainer (The Scripps Research Institute), and Andrej Sali (University of California at San Francisco) and wwPDB Representatives Helen Berman (RCSB PDB), Stephen Burley (RCSB PDB), Gerard Kleywegt (PDBe), John Westbrook (RCSB PDB), and Cathy Lawson (RCSB PDB) </p> <p> <a class="fancybox" rel="group" href="https://cdn.rcsb.org/wwpdb/img/task/sas-2014.jpg"> <img class="img-responsive img-thumbnail" src="https://cdn.rcsb.org/wwpdb/img/task/sas-2014.jpg" alt="SAS Task Force 2014 at Rutgers University" /> </a> <caption>SAS Task Force 2014 at Rutgers University</caption> </p> <p>An outcome of a project aimed to test and benchmark different approaches for modelling SAS profiles from PDB coordinates has been published:</p> <p>A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking<br/> Trewhella, J., Vachette, P., Bierma, J., Blanchet, C., Brookes, E., Chakravarthy, S., Chatzimagas, L., Cleveland, T. E., Cowieson, N., Crossett, B., Duff, A. P., Franke, D., Gabel, F., Gillilan, R. E., Graewert, M., Grishaev, A., Guss, J. M., Hammel, M., Hopkins, J., Huang, Q., Hub, J. S., Hura, G. L., Irving, T. C., Jeffries, C. M., Jeong, C., Kirby, N., Krueger, S., Martel, A., Matsui, T., Li, N., Perez, J., Porcar, L., Prange, T., Rajkovic, I., Rocco, M., Rosenberg, D. J., Ryan, T. M., Seifert, S., Sekiguchi, H., Svergun, D., Teixeira, S., Thureau, A., Weiss, T. M., Whitten, A. E., Wood, K. & Zuo, X. (2022) <i>Acta Cryst</i>. D78: 1315-1336 doi: <a href="https://doi.org/10.1107/S2059798322009184" target="_blank">10.1107/S2059798322009184</a> </p> <p>In total, 171 SAXS and 76 SANS measurements for five proteins (ribonuclease A, lysozyme, xylanase, urate oxidase and xylose isomerase) were collected and analysed centrally. In the process, new methods for data comparing and merging were developed. The data produced for this effort, has been deposited in the <a href="https://www.sasbdb.org/" target="_blank">SAS Biological Data Bank (SASBDB)</a> as consensus data along with the contributing individual data sets.</p> <p>A chapter describing the work done to establish the 2017 publication guidelines for biomolecular SAS, the establishment of the SASBDB, and the evolution and outcomes of the benchmarking project has been published:</p> <p>Chapter One - Data quality assurance, model validation, and data sharing for biomolecular structures from small-angle scattering <br/> Jill Trewhella (2023) <i>Methods</i> in Enzymology 678: 1-22 doi: <a href="https://doi.org/10.1016/bs.mie.2022.11.002" target="_blank">10.1016/bs.mie.2022.11.002</a> </p> <p>An updated template reporting table for biomolecular SAXS data has been published:</p> <p>2023 update of template tables for reporting biomolecular structural modelling of small-angle scattering data<br/> J. Trewhella, C. M. Jeffries and A. E. Whitten (2023) <i>Acta Cryst.</i> D79: 122-132 doi: <a href="https://doi.org/10.1107/S2059798322012141" target="_blank">10.1107/S2059798322012141</a> </p>  </div> </div> </div> <br> <footer class="footer"> <div class="container-fluid hidden-print" style="position: relative;"> <div class="row topFooter tinyPad"> <div class="ScreenLimitFooter"> <div class="col-sm-4"> <div class="smallMarginTop"> <a href="https://www.facebook.com/pages/Worldwide-PDB/223648640998643" target="_blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/facebook.png" width="24" height="24"></a> <a href="https://www.youtube.com/channel/UCgM7zpapumhWHDMV11FIz0Q" target="_blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/youtube-logo.png" width="24" height="24"></a> <a href="#"><img alt="RSS Feed for the Latest News" src="https://cdn.rcsb.org/wwpdb/img/core/rss.png" width="24" height="24"></a> <a href="mailto: info@wwpdb.org"><img src="https://cdn.rcsb.org/wwpdb/img/core/mail.png" width="24" height="24"></a> </div> <div class="smallMarginTop"> <a href="/news/news.php"> <p><a href="/news/news.php">News & Announcements</a></p> </a> </div> <div> <p><a href="https://lists.wwpdb.org/list/pdb-l.lists.wwpdb.org">Community Bulletin Board</a></p> </div> <div><a class='brand hidden-desktop' href='http://foundation.wwpdb.org/' target='_blank'><img src="https://cdn.rcsb.org/wwpdb/img/core/wwpdb-foundation-logo.png" class="logoLimit smallMarginTop"></a></div> </div> <div class="col-sm-4"> <div class="tinyMarginTop"> <h4><a class="h4-link" href="/download/downloads.php">Download Archive</a></h4> </div> <div class="smallMarginTop"> <a href="https://files.wwpdb.org/pub/pdb/">RCSB PDB</a> | <a href="https://ftp.ebi.ac.uk/pub/databases/pdb/">PDBe</a> | <a href="https://ftp.pdbj.org/pub/pdb/">PDBj</a> <br> <a href="/download/downloads.php">Instructions</a> </div> <div class="row"> <div class="col-sm-4"> <div class="tinyMarginTop"> <h4>Archive Snapshots</h4> </div> <div class="smallMarginTop"> <a href="https://s3snapshots.rcsb.org">RCSB PDB (https)</a> | <a href="ftp://snapshots.pdbj.org/">PDBj</a> </div> </div>  </div> </div> <div class="col-sm-3"> <h4> Cite wwPDB: </h4> <div class="smallMarginTop"> <em>Nature Structural Biology</em> <strong>10</strong>, 980 (2003)<br> <a href="http://dx.doi.org/10.1038/nsb1203-980" target="_blank">doi: 10.1038/nsb1203-980</a> <p class="tinyMarginTop"><a href="/about/publications.php">More publications</a></p> </div> </div> <div class="row" style="padding: 40px 0px 10px 10px"> <div class="col-sm-7"> <div class="tinyPad"> <h4>wwPDB Members:</h4> </div> <div class="col-sm-2 tinyPad"><a href="https://www.rcsb.org/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/rcsb-pdb.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="http://bmrb.io/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/bmrb.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="https://www.ebi.ac.uk/pdbe/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/pdbe.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="https://www.ebi.ac.uk/pdbe/emdb/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/emdb.png" class="logoLimit img-responsive"></a></div> <div class="col-sm-2 tinyPad"><a href="https://www.pdbj.org/" target="blank"><img src="https://cdn.rcsb.org/wwpdb/img/core/pdbj.png" class="logoLimit img-responsive"></a></div> </div> <div class="col-sm-1"><br></br></div> <div class="col-sm-4"> <div class="row"> <div class="col-xs-6"> <a href='http://www.CoreTrustSeal.org' target='_blank'><img src="https://cdn.rcsb.org/wwpdb/img/homepage/CoreTrustSeal-logo-transparent-small.png" class='img-responsive seal' style="border-right: 1px solid #666; 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wwPDB: Small Angle Scattering (SAS)