PDBx/mmCIF References

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class="row"> <h2>PDBx/mmCIF References </h2> </div> <div class="row"> <ul class="ul-lg"> <li>J. D. Westbrook, J. Y. Young, C. Shao, Z. Feng, V. Guranovic, C. L. Lawson, B. Vallat, P. D. Adams, J. M. Berrisford, G. Bricogne, K. Diederichs, R. P. Joosten, P. Keller, N. W. Moriarty, O. V. Sobolev, S. Velankar, C. Vonrhein, D. G. Waterman, G. Kurisu, H. M. Berman, S. K. Burley, E. Peisach. <a href="https://www.sciencedirect.com/science/article/pii/S0022283622001796?via%3Dihub" target="_blank"> PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology</a>, <i>Journal of Molecular Biology</i> (2022) 434(11):167599</li> <li> Chapter 10 The PDB format, mmCIF formats, and other data formats. In Structural Bioinformatics, J. D. Westbrook, P. M. D. Fitzgerald. (2009). Second Edition (P. E. Bourne & J. Gu, eds.), pp. 271-291. John Wiley & Sons, Inc., Hoboken, New Jersey.</li> <li><a href="/docs/pubs/AUTHOR_ch3o6.pdf" target="_blank"> Chapter 3.6. Classification and use of macromolecular data.</a> (PDF) in <i>International Tables for Crystallography G.</i> Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. 2005, Springer: Dordrecht, The Netherlands. p. 144-198. </li> <li><a href="/docs/pubs/appendix3.6.3_pdbx.pdf" target="_blank"> Chapter 3.6.2 The Protein Data Bank exchange dictionary (PDF) </a> Westbrook J, Henrick K, Ulrich EL, Berman HM. (2005). in <i>International Tables for Crystallography G.</i> Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors, Springer: Dordrecht, The Netherlands. p. 195-198.</li> <li> <a href="/docs/pubs/AUTHOR_ch4o5.pdf">Chapter 4.5. The Macromolecular dictionary (mmCIF)</a> Fitzgerald PMD, Westbrook JD, Bourne PE, McMahon B, Watenpaugh KD, Berman HM. (2005). in <i>International Tables for Crystallography</i>, G. Definition and exchange of crystallographic data, S.R. Hall and B. McMahon, Editors. Springer: Dordrecht, The Netherlands. pp. 295-443. </li> <li> Chapter 2.6 Specification of a relational Dictionary Definition Language (DDL2). J. D. Westbrook, H. M. Berman, S. R. Hall. (2005). in <i>International Tables for Crystallography</i> (S. R. Hall & B. McMahon, eds.), Vol. G. Definition and exchange of crystallographic data, pp. 61-72. Springer, Dordrecht, The Netherlands.</li> <li> Chapter 5.5 The use of mmCIF architecture for PDB data management. Westbrook J, Yang H, Feng Z, Berman HM. (2005). in <i> International Tables for Crystallography</i> (S. R. Hall & B. McMahon, eds.), Vol. G. Definition and exchange of crystallographic data, pp. 539-543. Springer, Dordrecht, The Netherlands. </i> <li> PDBML: the representation of archival macromolecular structure data in XML. John Westbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick and Helen M. Berman, <a href="http://bioinformatics.oupjournals.org/cgi/content/abstract/bti082" target="_blank"> Bioinformatics, 21(7), 988-992, 2005.</a> </li> <li> STAR/mmCIF: An Extensive Ontology for Macromolecular Structure and Beyond (PDF) <a href="/docs/pubs/bioinfo00.pdf"> Westbrook J, Bourne PE. <i>Bioinformatics</i> (2000) 16(2), 159-168.</a></li> <li> J. D. Westbrook, S.-H. Hsieh, P. M. D. Fitzgerald. CIF Applications. VI. <I>CIFLIB</I>: an application-program interface to CIF dictionaries and data files. <I>J. Appl. Cryst.</I> (1997) <B>30</B>, 79-83.</li> <li> The Macromolecular Crystallographic Information File (mmCIF) <a href="/docs/pubs/methods-enzymology-paper-1997.html"><i>Meth. Enzymol.</i> (1997) 277, 571-590. </a></li> <li> How the Nucleic Acid Database Uses CIF. H. M. Berman and J. D. Westbrook, in <i>Proceedings of the First Macromolecular CIF Tools Workshop</i>, P. E. Bourne, ed. (1993) National Science Foundation, Tarrytown, New York, p. 65.</li> <li>The STAR File: a New Format for Electronic Data Transfer and Archiving, S. R. Hall, <i>J. Chem. Inf. Comp. Sci.</i> (1991) <b>31</b>, 326-333.</li> <li> The Crystallographic Information file (CIF): a New Standard Archive File for Crystallography, S. R. Hall, A. H. Allen, and I. D. Brown, <i>Acta Cryst.</i> (1991) <b>A47</b>, 655-685.</li> </ul> </div> </div>  </div>   <script src="/assets/js/jquery/core/jquery-1.11.0.min.js" ></script> <script src="/assets/css/bootstrap/js/bootstrap.js" > </script>  <script src="/js/MyApp.js"></script>   <div id="footer"> <div class="container"> <p class="muted credit">© wwPDB </p> </div> </div>  </body> </html>

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PDBx/mmCIF References