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<p><font size="4">Virtual Crash Course<br>
The RCSB Protein Data Bank will provide a course, "Use PDB data
to their full extent: Understanding PDBx/mmCIF" on Wednesday,
May 3rd 2023 from 1:00-3:00 EDT<br>
<br>
Understand the basics of PDBx/mmCIF data dictionary and file
format that underpin archiving of more than 200,000
experimentally determined three-dimensional biostructures in the
PDB. Learn about software tools for generating and working with
PDBx/mmCIF files, and programmatic access for harvesting PDB
data.<br>
<br>
The program:
<a class="moz-txt-link-freetext" href="https://iqb.rutgers.edu/sites/iqb.rutgers.edu/files/crashcourses/mmCIF-crash-course.pdf">https://iqb.rutgers.edu/sites/iqb.rutgers.edu/files/crashcourses/mmCIF-crash-course.pdf</a><br>
<br>
Free registration: <a class="moz-txt-link-freetext" href="https://go.rutgers.edu/u3vpwjet">https://go.rutgers.edu/u3vpwjet</a><br>
<br>
If you have questions, please contact Michelle Sanghera:
<a class="moz-txt-link-abbreviated" href="mailto:msanghera@iqb.rutgers.edu">msanghera@iqb.rutgers.edu</a></font></p>
<p><br>
</p>
<div class="moz-cite-prefix">On 3/10/23 08:29, Chenghua Shao wrote:<br>
</div>
<blockquote type="cite"
cite="mid:fbe12062-9cdf-231f-2a7b-735829ee9053@rcsb.rutgers.edu">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div class="moz-text-flowed" style="font-size: 16px;"
lang="x-unicode"><b>Use PDB data to their full extent:
Understanding PDBx/mmCIF </b><br>
<br>
Wednesday, May 3rd 2023 | 1:00 PM EDT <br>
<br>
Registration: go.rutgers.edu/u3vpwjet <a
class="moz-txt-link-rfc2396E"
href="https://go.rutgers.edu/u3vpwjet" moz-do-not-send="true"><https://go.rutgers.edu/u3vpwjet></a>
<br>
<br>
<br>
* This RCSB Protein Data Bank (PDB) virtual course will be
broadcast on Zoom. Please fill out the registration form to
receive the Zoom link. Registration will be available online
from March 1, 2023 to May 3, 2023. <br>
<br>
</div>
<div class="moz-text-flowed" style="font-size: 16px;"
lang="x-unicode"><br>
</div>
<div class="moz-text-flowed" style="font-size: 16px;"
lang="x-unicode">LEARNING OBJECTIVES <br>
<br>
Understand the basics of PDBx/mmCIF data dictionary and file
format that underpin archiving of more than 200,000
experimentally determined three-dimensional biostructures in the
PDB. Learn about software tools for generating and working with
PDBx/mmCIF files, and programmatic access for harvesting PDB
data. Main topics: <br>
<br>
* PDBx/mmCIF format description and examples <br>
* PDBx/mmCIF data model <br>
* Software tools for generating, editing, and visualizing
PDBx/mmCIF files <br>
* PDBx/mmCIF dictionary extensions, including ModelCIF for
computed <br>
structure models (CSM) from AI/ML <br>
* Parsing data from PDBx/mmCIF files for your research <br>
<br>
<br>
<br>
<b>WHO SHOULD ATTEND </b><br>
<br>
Professionals and graduate students interested in learning about
strategies to take full advantage of PDB data in the fields of:
<br>
<br>
* Structural biology <br>
* Cheminformatics and computational chemistry <br>
* Bioinformatics and computational biology <br>
<br>
<br>
<br>
<b>PROGRAM</b> | Download Printable Program <a
class="moz-txt-link-rfc2396E"
href="https://iqb.rutgers.edu/sites/iqb.rutgers.edu/files/crashcourses/mmCIF-crash-course.pdf"
moz-do-not-send="true"><https://iqb.rutgers.edu/sites/iqb.rutgers.edu/files/crashcourses/mmCIF-crash-course.pdf></a>
<br>
<br>
<br>
1:00–1:10 PM <span class="moz-txt-slash"><span
class="moz-txt-tag"></span>Welcome<span class="moz-txt-tag"></span></span><br>
Stephen K. Burley, M.D., D.Phil. <br>
Director, RCSB PDB and Founding Director, <br>
Institute for Quantitative Biomedicine, Rutgers University <br>
<br>
1:10–1:25 PM Introduction and course objectives <br>
<i class="moz-txt-slash"><span class="moz-txt-tag"></span></i><span
class="moz-txt-slash">Gregg Crichlow, Ph.D., RCSB PDB, Rutgers
University</span><i class="moz-txt-slash"><span
class="moz-txt-tag"></span></i><br>
<br>
1:25–1:45 PM PDBx/mmCIF format - Not your parents’ legacy PDB
format <br>
Ezra Peisach, Ph.D., RCSB PDB, Rutgers University <br>
<br>
1:45–2:05 PM PDBx/mmCIF data files - Lifting the lid off the
black box <br>
Brian Hudson, Ph.D., RCSB PDB, Rutgers University <br>
<br>
2:05–2:50 PM Programmatic data access and analysis using
PDBx/mmCIF files <br>
Irina Persikova, Ph.D. and Chenghua Shao, Ph.D., <br>
RCSB PDB, Rutgers University <br>
<br>
2:50–3:00 PM Closing remarks and acknowledgements <br>
Stephen K. Burley, M.D., D.Phil. <br>
<br>
<br>
Development and management of the PDBx/mmCIF data dictionary is
a collaborative effort involving RCSB PDB, Worldwide Protein
Data Bank (wwPDB, wwPDB.org <a class="moz-txt-link-rfc2396E"
href="http://www.wwpdb.org/" moz-do-not-send="true"><http://www.wwpdb.org/></a>)
partners, and members of the wwPDB PDBx/mmCIF Working Group
(wwpdb.org/task/mmcif <a class="moz-txt-link-rfc2396E"
href="https://www.wwpdb.org/task/mmcif" moz-do-not-send="true"><https://www.wwpdb.org/task/mmcif></a>).
<br>
<br>
<br>
<b class="moz-txt-star"><span class="moz-txt-tag"></span>CO-ORGANIZERS<span
class="moz-txt-tag"></span></b> <br>
<br>
RCSB PDB Biocurators: Gregg Crichlow, Justin Flatt, Sutapa
Ghosh, Brian Hudson, Yuhe Liang, Ezra Peisach, Irina Persikova,
Monica Sekharan, Chenghua Shao, Jasmine Young <br>
(Rutgers, The State University of New Jersey). <br>
</div>
<div class="moz-text-flowed" style="font-size: 16px;"
lang="x-unicode"><br>
</div>
<div class="moz-text-flowed" style="font-size: 16px;"
lang="x-unicode"><br>
</div>
<div class="moz-text-flowed" style="font-size: 16px;"
lang="x-unicode"><b>QUESTIONS</b></div>
<div class="moz-text-flowed" style="font-size: 16px;"
lang="x-unicode"><br>
</div>
<div class="moz-text-flowed" style="font-size: 16px;"
lang="x-unicode">Contact Michelle Sanghera <a
class="moz-txt-link-abbreviated moz-txt-link-freetext"
href="mailto:msanghera@iqb.rutgers.edu" moz-do-not-send="true">msanghera@iqb.rutgers.edu</a>
<br>
<br>
<br>
<b>CO-SPONSORS </b><br>
<b> </b></div>
<div class="moz-text-flowed" style="font-size: 16px;"
lang="x-unicode"><br>
<b class="moz-txt-star"><span class="moz-txt-tag"></span>RCSB
Protein Data Bank<span class="moz-txt-tag"></span></b> <br>
rcsb.org <a class="moz-txt-link-rfc2396E"
href="https://www.rcsb.org/" moz-do-not-send="true"><https://www.rcsb.org/></a><br>
RCSB PDB is managed by Rutgers, UCSD/SDSC, and UCSF. <br>
RCSB PDB is supported by grants from the NSF (DBI-1832184), the
US DoE (DE-SC0019749), and the NIH (R01GM133198). <br>
RCSB PDB is a founding member of the wwPDB. <br>
<br>
<b class="moz-txt-star"><span class="moz-txt-tag"></span>Institute
for Quantitative Biomedicine<span class="moz-txt-tag"></span></b>
<br>
</div>
<div class="moz-text-flowed" style="font-size: 16px;"
lang="x-unicode">iqb.rutgers.edu <a
class="moz-txt-link-rfc2396E" href="https://iqb.rutgers.edu/"
moz-do-not-send="true"><https://iqb.rutgers.edu/></a></div>
<br>
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