PDB-101: Train: All Training Courses

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<div onclick="location.href="/train/pdb-and-data-archiving-curriculum/about"" class="pdb101-left-menu-item"> <div class="pdb101-left-menu-item-text">PDB and Data Archiving Curriculum</div> <div class="pdb101-left-menu-item-chevron"><span class="fa fa-chevron-right fade"></span></div> </div> </div> </div> <div class="col-xs-12 col-sm-12 col-md-9 pdb101-page-content"> <div class="row grid-list-btns"> <div class="col-xs-12 col-sm-9"> <h1>Train: All Training Courses</h1> </div> <div class="col-xs-12 col-sm-3 text-right"> <div role="group" class="btn-group"> <button id="grid-btn" type="button" onclick="toggleGridList("grid")" class="btn btn-default btn-sm active"><img src='https://cdn.rcsb.org/pdb101/common/images/grid.png'>Grid</button> <button id="list-btn" type="button" onclick="toggleGridList("list")" class="btn btn-default btn-sm"><img src='https://cdn.rcsb.org/pdb101/common/images/list.png'>List</button> </div> </div> </div> <div class="row grid-view"> <div class="col-xs-6 col-sm-4 col-md-3 grid-cell"><a href="/train/training-events/enzymology2" class="no-underline"><img src="https://cdn.rcsb.org/pdb101/train/enzymology2/enzymology-icon.png" class="icon"> <div>Teaching Enzymology with the Protein Data Bank: From Pandemic to Paxlovid (2024)</div></a></div> <div class="col-xs-6 col-sm-4 col-md-3 grid-cell"><a href="/train/training-events/validation" class="no-underline"><img src="https://cdn.rcsb.org/pdb101/train/validation/validation-icon.png" class="icon"> <div>Understanding PDB Validation: Which experimental structures should I rely on?</div></a></div> <div class="col-xs-6 col-sm-4 col-md-3 grid-cell"><a href="/train/training-events/csm2" class="no-underline"><img src="https://cdn.rcsb.org/pdb101/train/csm2/csm2-icon.png" class="icon"> <div>A Deep Dive into Computed Structure Model Exploration at RCSB.org</div></a></div> <div class="col-xs-6 col-sm-4 col-md-3 grid-cell"><a href="/train/training-events/molstar" class="no-underline"><img src="https://cdn.rcsb.org/pdb101/train/molstar/molstar-icon.png" class="icon"> <div>Visualize Biomolecular Structures with Mol*: From Atoms to Movies</div></a></div> <div class="col-xs-6 col-sm-4 col-md-3 grid-cell"><a href="/train/training-events/enzymology" class="no-underline"><img src="https://cdn.rcsb.org/pdb101/train/enzymology/enzymology-icon.png" class="icon"> <div>Teaching Enzymology with the Protein Data Bank: From Pandemic to Paxlovid (2023)</div></a></div> <div class="col-xs-6 col-sm-4 col-md-3 grid-cell"><a href="/train/training-events/api" class="no-underline"><img src="https://cdn.rcsb.org/pdb101/train/api/api-icon.png" class="icon"> <div>Leveraging RCSB PDB APIs for Bioinformatics Analyses and Machine Learning</div></a></div> <div class="col-xs-6 col-sm-4 col-md-3 grid-cell"><a href="/train/training-events/mmcif" class="no-underline"><img src="https://cdn.rcsb.org/pdb101/train/mmcif/mmcif-icon.png" class="icon"> <div>Use PDB data to their full extent: Understanding PDBx/mmCIF</div></a></div> <div class="col-xs-6 col-sm-4 col-md-3 grid-cell"><a href="/train/training-events/models" class="no-underline"><img src="https://cdn.rcsb.org/pdb101/train/models/models-icon.png" class="icon"> <div>Exploring Computed Structure Models on RCSB.org</div></a></div> <div class="col-xs-6 col-sm-4 col-md-3 grid-cell"><a href="/train/training-events/kbase" class="no-underline"><img src="https://cdn.rcsb.org/pdb101/train/kbase/kbase-icon.png" class="icon"> <div>Using KBase to access PDB Structures and Computed Structure Models</div></a></div> <div class="col-xs-6 col-sm-4 col-md-3 grid-cell"><a href="/train/training-events/python3" class="no-underline"><img src="https://cdn.rcsb.org/pdb101/train/python3/python3-icon.png" class="icon"> <div>Python Scripting for Molecular Docking | Part 3</div></a></div> <div class="col-xs-6 col-sm-4 col-md-3 grid-cell"><a href="/train/training-events/python2" class="no-underline"><img src="https://cdn.rcsb.org/pdb101/train/python2/python2-icon.png" class="icon"> <div>Python Scripting for Biochemistry & Molecular Biology | Part 2</div></a></div> <div class="col-xs-6 col-sm-4 col-md-3 grid-cell"><a href="/train/training-events/python" class="no-underline"><img src="https://cdn.rcsb.org/pdb101/train/python/python1-icon.png" class="icon"> <div>Python Scripting for Biochemistry & Molecular Biology | Part 1</div></a></div> <div class="col-xs-6 col-sm-4 col-md-3 grid-cell"><a href="/train/training-events/covid" class="no-underline"><img src="https://cdn.rcsb.org/pdb101/train/covid/covid-icon.png" class="icon"> <div>Boot Camp: COVID-19 Evolution and Structural Biology</div></a></div> </div> <div style="display:none;" class="list-view"> <table class="list-view"> <tr> <td class="tn"><a href="/train/training-events/enzymology2"><img src="https://cdn.rcsb.org/pdb101/train/enzymology2/enzymology-icon.png" class="icon"></a></td> <td> <h5><a href="/train/training-events/enzymology2" class="no-underline">Teaching Enzymology with the Protein Data Bank: From Pandemic to Paxlovid (2024)</a></h5><a href="/train/training-events/enzymology2" class="no-underline"></a> <p>In the second edition of this webinar, SARS-CoV-2 Main Protease is used to introduce and reinforce the use of RCSB.org resources for teaching protein structure and function.</p> </td> </tr> <tr> <td class="tn"><a href="/train/training-events/validation"><img src="https://cdn.rcsb.org/pdb101/train/validation/validation-icon.png" class="icon"></a></td> <td> <h5><a href="/train/training-events/validation" class="no-underline">Understanding PDB Validation: Which experimental structures should I rely on?</a></h5><a href="/train/training-events/validation" class="no-underline"></a> <p>Learn about primary PDB structure quality metrics, including those in the validation slider graphic; how PDB structure quality varies across the archive; and identify good structure(s) for research from RCSB.org.</p> </td> </tr> <tr> <td class="tn"><a href="/train/training-events/csm2"><img src="https://cdn.rcsb.org/pdb101/train/csm2/csm2-icon.png" class="icon"></a></td> <td> <h5><a href="/train/training-events/csm2" class="no-underline">A Deep Dive into Computed Structure Model Exploration at RCSB.org</a></h5><a href="/train/training-events/csm2" class="no-underline"></a> <p>Learn how to use RCSB.org features to navigate 3D predicted protein structures in the context of experimentally-determined PDB structures. Two case studies are provided: Low-density Lipoprotein Receptor Adapter Protein 1 (LDLRAP1) and Class II aminoacyl-tRNA synthetases.</p> </td> </tr> <tr> <td class="tn"><a href="/train/training-events/molstar"><img src="https://cdn.rcsb.org/pdb101/train/molstar/molstar-icon.png" class="icon"></a></td> <td> <h5><a href="/train/training-events/molstar" class="no-underline">Visualize Biomolecular Structures with Mol*: From Atoms to Movies</a></h5><a href="/train/training-events/molstar" class="no-underline"></a> <p>Mol* (MolStar) is a web application available on RCSB.org designed for visualizing biomolecular structures in 3D.</p> </td> </tr> <tr> <td class="tn"><a href="/train/training-events/enzymology"><img src="https://cdn.rcsb.org/pdb101/train/enzymology/enzymology-icon.png" class="icon"></a></td> <td> <h5><a href="/train/training-events/enzymology" class="no-underline">Teaching Enzymology with the Protein Data Bank: From Pandemic to Paxlovid (2023)</a></h5><a href="/train/training-events/enzymology" class="no-underline"></a> <p>This webinar uses the example of SARS-CoV-2 Main Protease to introduce or reinforce the use of RCSB.org resources for teaching protein structure and function.</p> </td> </tr> <tr> <td class="tn"><a href="/train/training-events/api"><img src="https://cdn.rcsb.org/pdb101/train/api/api-icon.png" class="icon"></a></td> <td> <h5><a href="/train/training-events/api" class="no-underline">Leveraging RCSB PDB APIs for Bioinformatics Analyses and Machine Learning</a></h5><a href="/train/training-events/api" class="no-underline"></a> <p>This course introduces users to the two main APIs that power the RCSB.org website: Data API and Search API. The live course consisted of two parts: <strong>Part 1</strong> featured lectures that introduced the APIs (October 12), while <strong>Part 2</strong> featured hands-on sessions held twice (October 19 and Otober 24). The hands-on session consisted of two coding examples demonstrations followed by hands-on coding in break out rooms. Only the coding demonstrations from Part 2 are available in this online course.</p> </td> </tr> <tr> <td class="tn"><a href="/train/training-events/mmcif"><img src="https://cdn.rcsb.org/pdb101/train/mmcif/mmcif-icon.png" class="icon"></a></td> <td> <h5><a href="/train/training-events/mmcif" class="no-underline">Use PDB data to their full extent: Understanding PDBx/mmCIF</a></h5><a href="/train/training-events/mmcif" class="no-underline"></a> <p>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. </p> </td> </tr> <tr> <td class="tn"><a href="/train/training-events/models"><img src="https://cdn.rcsb.org/pdb101/train/models/models-icon.png" class="icon"></a></td> <td> <h5><a href="/train/training-events/models" class="no-underline">Exploring Computed Structure Models on RCSB.org</a></h5><a href="/train/training-events/models" class="no-underline"></a> <p>In August 2022, the RCSB PDB enabled access to ~1 million Computed Structure Models (CSMs) from AlphaFoldDB and RoseTTAFold in addition to the ~200,000 experimentally-determined PDB structures on the RCSB.org website. A Virtual Crash Course was held to inform the RCSB.org users how to search, visualize, and analyze CSMs alongside experimentally-determined PDB structures using the custom-developed RCSB PDB tools.</p> </td> </tr> <tr> <td class="tn"><a href="/train/training-events/kbase"><img src="https://cdn.rcsb.org/pdb101/train/kbase/kbase-icon.png" class="icon"></a></td> <td> <h5><a href="/train/training-events/kbase" class="no-underline">Using KBase to access PDB Structures and Computed Structure Models</a></h5><a href="/train/training-events/kbase" class="no-underline"></a> <p>At this virtual course, the participants had the opportunity to learn about the protein structure-related tools, visualizations, and workflows that have been integrated into DOE KBase. This course was organized jointly by RCSB PDB and DOE KBase.</p> </td> </tr> <tr> <td class="tn"><a href="/train/training-events/python3"><img src="https://cdn.rcsb.org/pdb101/train/python3/python3-icon.png" class="icon"></a></td> <td> <h5><a href="/train/training-events/python3" class="no-underline">Python Scripting for Molecular Docking | Part 3</a></h5><a href="/train/training-events/python3" class="no-underline"></a> <p>In this workshop, Python scripting and libraries are used to explore ligand binding to enzymes. The corresponding Jupyter notebooks are customizable for individual research and teaching purposes. This course was developed by Paul A. Craig (Rochester Institute of Technology) and Jessica A. Nash (Molecular Sciences Software Institute).</p> </td> </tr> <tr> <td class="tn"><a href="/train/training-events/python2"><img src="https://cdn.rcsb.org/pdb101/train/python2/python2-icon.png" class="icon"></a></td> <td> <h5><a href="/train/training-events/python2" class="no-underline">Python Scripting for Biochemistry & Molecular Biology | Part 2</a></h5><a href="/train/training-events/python2" class="no-underline"></a> <p>This is the second part of the IQB Crash Course designed to introduce life scientists to the power and flexibility of solving problems with Python. This course offers a brief review of Python and the Jupyter Notebook environment first, later diving into working with Python libraries and various types of data.</p> </td> </tr> <tr> <td class="tn"><a href="/train/training-events/python"><img src="https://cdn.rcsb.org/pdb101/train/python/python1-icon.png" class="icon"></a></td> <td> <h5><a href="/train/training-events/python" class="no-underline">Python Scripting for Biochemistry & Molecular Biology | Part 1</a></h5><a href="/train/training-events/python" class="no-underline"></a> <p>This workshop familiarizes life scientists with the power and flexibility of solving problems with Python by introducing specific coding skills, as well as providing insight into the broader array of open-access resources and libraries that are available for scientific computation. This course was presented by Paul A. Craig, Professor of Biochemistry, Rochester Institute of Technology (RIT) and Jessica A. Nash, Software Scientist, Molecular Sciences Software Institute (MolSSI)</p> </td> </tr> <tr> <td class="tn"><a href="/train/training-events/covid"><img src="https://cdn.rcsb.org/pdb101/train/covid/covid-icon.png" class="icon"></a></td> <td> <h5><a href="/train/training-events/covid" class="no-underline">Boot Camp: COVID-19 Evolution and Structural Biology</a></h5><a href="/train/training-events/covid" class="no-underline"></a> <p>These materials were used in a June 2020 Boot Camp for undergraduate researchers held virtually to understand how the protein evolved during the first six months of the COVID-19 pandemic by exploring amino acid sequence and 3D atomic-level structure using various structural bioinformatics tools.</p> </td> </tr> </table> </div> <div class="row"> <div class="col-sm-12"> <p><a href="https://view.forms.app/rcsb-pdb/training-announcements">Sign up</a> to receive email notifications about upcoming training courses. </p> </div> </div> </div> </div> </div> <div id="footer_main" class="hidden-print"> <div class="container"> <div class="row"> <div class="col-sm-12 col-md-7"> <p><strong>About PDB-101</strong></p> <p>Researchers around the globe make 3D structures freely available from the Protein Data Bank (PDB) archive. PDB-101 training materials help graduate students, postdoctoral scholars, and researchers use PDB data and RCSB PDB tools. Outreach content demonstrate how PDB data impact fundamental biology, biomedicine, bioengineering/biotechnology, and energy sciences in 3D for a diverse and multidisciplinary user community. Education Materials provide lessons and activities for teaching and learning.</p> <p>PDB-101 is developed by the <a href="https://rcsb.org" target="_blank">RCSB PDB</a>.</p> </div> <div class="col-sm-12 col-md-5 text-center"> <p>RCSB PDB (<a href="http://nar.oxfordjournals.org/content/28/1/235.abstract" target="blank">citation</a>) is hosted by</p><img src="//cdn.rcsb.org/pdb101/common/images/Logo_Rutgers-2024.png" alt="Rutgers University logo" usemap="#rutgers-map" height="32" style="padding:0px 10px; border-right: 1px solid #000000;"><img src="//cdn.rcsb.org/pdb101/common/images/Logo_UCSD-SDSC.png" alt="University of California San Diego/San Diego Supercomputer Center logos" usemap="#UCSD-SDSC-map" height="26" style="padding: 0px 10px; border-right: 1px solid #000000;"><img src="//cdn.rcsb.org/pdb101/common/images/Logo_UCSF.png" alt="Univesity of California San Franciscologo" usemap="#UCSF-map" height="26" style="padding-left: 10px;"><map name="rutgers-map"> <area shape="rect" coords="0,0,115,26" href="http://www.rutgers.edu/" alt="Rutgers" target="_blank"></map><map name="UCSD-SDSC-map"> <area shape="rect" coords="0,0,150,26" href="http://ucsd.edu/" alt="UCSD" target="_blank"> <area shape="rect" coords="151,0,255,26" href="http://www.sdsc.edu/" alt="SDSC" target="_blank"></map><map name="UCSF-map"> <area shape="rect" coords="0,0,64,26" href="http://www.ucsf.edu/" alt="UCSF" target="_blank"></map><br><br> <p>RCSB PDB is a member of <span id='pdbmembers_footer'><a href='http://www.wwpdb.org/' target='_blank'><img src='//cdn.rcsb.org/pdb101/common/images/Logo_wwpdb.png' width='70'></a><span class='pipe'></span><a href='http://www.emdatabank.org/' target='_blank'><img src='https://cdn.rcsb.org/pdb101/common/images/EMDataResourcelogo.png' width='100'></a></p> </div> </div> </div> </div> <div id="footer_grant" class="hidden-print"> <div class="container"> <div class="row"> <p>RCSB PDB Core Operations are funded by the <a href="http://www.nsf.gov/" target="_blank">U.S. National Science Foundation</a> (DBI-2321666), the <a href="http://science.energy.gov/" target="_blank">US Department of Energy</a> (DE-SC0019749), and the <a href="http://www.cancer.gov/" target="_blank">National Cancer Institute</a>, <a href="http://www.niaid.nih.gov/" target="_blank">National Institute of Allergy and Infectious Diseases</a>, and <a href="http://www.nigms.nih.gov/" target="_blank">National Institute of General Medical Sciences</a> of the <a href="http://www.nih.gov/" target="_blank">National Institutes of Health</a> under grant R01GM157729.</p> </div> </div> </div> <div id="jira-fdbck"></div><script> //Google Analytics tracking code {/* (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){ (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o), m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m) })(window,document,'script','//www.google-analytics.com/analytics.js','ga'); ga('create', 'UA-71059016-1', 'auto'); ga('send', 'pageview'); */} </script> </div> </body> </html>

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