PDB-101: Virtual Crash Course

<!DOCTYPE html> <html> <head> <script src="https://www.googletagmanager.com/gtag/js?id=G-EPQ9202NVY" async></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); //- gtag('config', 'UA-71059016-1'); gtag('config', 'G-EPQ9202NVY'); </script> <title>PDB-101: Virtual Crash Course</title> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1"> <meta property="og:title" content="PDB101: Virtual Crash Course"> <meta property="og:description" content="PDB-101: Training, Outreach, and Education portal of RCSB PDB"> <meta property="og:image" content="https://cdn.rcsb.org/news/2023/train-resources-panel.png"> <meta property="og:site_name" content="RCSB: PDB-101"> <meta name="twitter:card" content="summary"> <meta name="twitter:title" content="PDB101: Virtual Crash Course"> <meta name="twitter:description" content="PDB-101: Training, 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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> <p>After watching the videos featured in this course, you will be able to: </p> <ul> <li>Extract data and build dataframes using the Pandas library</li> <li>Perform curve fitting with enzyme kinetics data</li> <li>Extract data from mmCIF files (the native Protein Data Bank data file format) using the Biopython library</li> <li>Extract data from mmCIF files using the RCSB PDB API</li> </ul> <p>Additional materials for this course are available: <ul> <li> <a href="http://education.molssi.org/python-scripting-biochemistry/chapters/introduction.html">Jupyter book for the full Python Scripting for Biochemistry & Molecular Biology Workshop</a></li> </ul> </p> <p>Click on the image below to play the video.</p> <div class="row"> <div class="col-xs-5"> <img src="https://cdn.rcsb.org/pdb101/train/python2/video1.png" ytVideoId="2rw58tfK8zs" class="img-responsive marginBottom watch"> </div> <div style="padding:10px 0 0 0" class="col-xs-7"> <h5>Part 2 Introduction</h5> <p class="noMargin boldText">Stephen K. Burley</p> <p>Director, RCSB Protein Data Bank</p> </div> </div> <div class="row"> <div class="col-xs-5"> <img src="https://cdn.rcsb.org/pdb101/train/python2/video2.png" ytVideoId="EyBnZcJgelM" class="img-responsive marginBottom watch"> </div> <div style="padding:10px 0 0 0" class="col-xs-7"> <h5>Python Primer: Review of Python and the Jupyter Notebook environment</h5> <p class="noMargin boldText">Jessica A. Nash</p> <p>Software Scientist, Molecular Sciences Software Institute (MolSSI)</p> </div> </div> <div class="row"> <div class="col-xs-5"> <img src="https://cdn.rcsb.org/pdb101/train/python2/video3.png" ytVideoId="cCYu4QlejD8" class="img-responsive marginBottom watch"> </div> <div style="padding:10px 0 0 0" class="col-xs-7"> <h5>Nonlinear regression: Creating the Pandas DataFrame</h5> <p class="noMargin boldText">Paul A. Craig</p> <p>Professor of Biochemistry, Rochester Institute of Technology (RIT)</p> </div> </div> <div class="row"> <div class="col-xs-5"> <img src="https://cdn.rcsb.org/pdb101/train/python2/video4.png" ytVideoId="5Zr_8b-aHx4" class="img-responsive marginBottom watch"> </div> <div style="padding:10px 0 0 0" class="col-xs-7"> <h5>Nonlinear regression: Curve fitting</h5> <p class="noMargin boldText">Paul A. Craig</p> <p>RIT</p> </div> </div> <div class="row"> <div class="col-xs-5"> <img src="https://cdn.rcsb.org/pdb101/train/python2/video5.png" ytVideoId="dWqvNQuInjA" class="img-responsive marginBottom watch"> </div> <div style="padding:10px 0 0 0" class="col-xs-7"> <h5>Extracting data from mmCIF files using the Biopython library</h5> <p class="noMargin boldText">Jessica A. Nash</p> <p>MolSSI</p> </div> </div> <div class="row"> <div class="col-xs-5"> <img src="https://cdn.rcsb.org/pdb101/train/python2/video6.png" ytVideoId="LC9dkM7y7dM" class="img-responsive marginBottom watch"> </div> <div style="padding:10px 0 0 0" class="col-xs-7"> <h5>Extracting data from mmCIF files using the RCSB PDB API</h5> <p class="noMargin boldText">Jessica A. Nash</p> <p>MolSSI</p> </div> </div> </div> </div> <div id="myModal" class="modal videoModal"> <div id="myModalContent" class="modal-content videoModal-content"> <div id="myModalHeader" class="modal-header"><span id="myClose" class="close">×</span></div> <div id="myModalBody" class="modal-body"> </div> </div> </div> <script> const videoThumbnails = document.getElementsByClassName('watch'); const myModal = document.getElementById('myModal'); const myModalBody = document.getElementById('myModalBody'); const myClose = document.getElementById('myClose'); for(const videoThumbnail of videoThumbnails){ videoThumbnail.addEventListener('click', function(e) { myModal.style.visibility = 'visible' myModal.style.display = 'block'; myModalBody.innerHTML = ''; const videoIframe = document.createElement('iframe'); Object.assign(videoIframe, { className: 'embed-responsive-item', type: 'movie', src: 'https://www.youtube.com/embed/' + e.target.getAttribute('ytVideoId'), height: 480, width: 853, frameborder: 0, allowfullscreen: '', }) const myVideodiv = document.createElement('div') myVideodiv.className = 'responsive-container' myModalBody.appendChild(myVideodiv) myVideodiv.appendChild(videoIframe) }) } myClose.onclick = closeModalStopVideo window.onclick = function(event) { if (event.target === myModal){ closeModalStopVideo() } } function closeModalStopVideo(){ myModal.style.display = 'none' myModalBody.innerHTML = '' } </script> </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. 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PDB-101: Virtual Crash Course