Algorithm / en New algorithms by U of T researchers may revolutionize drug discoveries /news/new-algorithms-u-t-researchers-may-revolutionize-drug-discoveries <span class="field field--name-title field--type-string field--label-hidden">New algorithms by U of T researchers may revolutionize drug discoveries</span> <div class="field field--name-field-featured-picture field--type-image field--label-hidden field__item"> <img loading="eager" srcset="/sites/default/files/styles/news_banner_370/public/3d-ali.jpg?h=afdc3185&amp;itok=laVkH_sy 370w, /sites/default/files/styles/news_banner_740/public/3d-ali.jpg?h=afdc3185&amp;itok=yw8E6I0F 740w, /sites/default/files/styles/news_banner_1110/public/3d-ali.jpg?h=afdc3185&amp;itok=812gYFcZ 1110w" sizes="(min-width:1200px) 1110px, (max-width: 1199px) 80vw, (max-width: 767px) 90vw, (max-width: 575px) 95vw" width="740" height="494" src="/sites/default/files/styles/news_banner_370/public/3d-ali.jpg?h=afdc3185&amp;itok=laVkH_sy" alt="Ali Punjani"> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span>ullahnor</span></span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2017-02-06T11:14:36-05:00" title="Monday, February 6, 2017 - 11:14" class="datetime">Mon, 02/06/2017 - 11:14</time> </span> <div class="clearfix text-formatted field field--name-field-cutline-long field--type-text-long field--label-above"> <div class="field__label">Cutline</div> <div class="field__item">U of T PhD student Ali Punjani says the ability to determine the 3D structures of protein is critical in understanding how they work and how they will respond to drug therapies (photo by Ken Jones) </div> </div> <div class="field field--name-field-author-reporters field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/news/authors-reporters/don-campbell" hreflang="en">Don Campbell</a></div> </div> <div class="field field--name-field-author-legacy field--type-string field--label-above"> <div class="field__label">Author legacy</div> <div class="field__item">Don Campbell</div> </div> <div class="field field--name-field-topic field--type-entity-reference field--label-above"> <div class="field__label">Topic</div> <div class="field__item"><a href="/news/topics/breaking-research" hreflang="en">Breaking Research</a></div> </div> <div class="field field--name-field-story-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/news/tags/protein" hreflang="en">Protein</a></div> <div class="field__item"><a href="/news/tags/algorithm" hreflang="en">Algorithm</a></div> <div class="field__item"><a href="/news/tags/health" hreflang="en">Health</a></div> <div class="field__item"><a href="/news/tags/utsc" hreflang="en">UTSC</a></div> <div class="field__item"><a href="/news/tags/computer-science" hreflang="en">Computer Science</a></div> <div class="field__item"><a href="/news/tags/machine-learning" hreflang="en">machine learning</a></div> <div class="field__item"><a href="/news/tags/artificial-intelligence" hreflang="en">Artificial Intelligence</a></div> </div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>A new set of machine learning algorithms developed by U of T researchers that can generate 3D structures of tiny protein molecules may revolutionize the development of drug therapies for a range of diseases&nbsp;from Alzheimer’s to cancer.</p> <p>“Designing successful drugs is like solving a puzzle,” says U of T PhD student <strong>Ali Punjani</strong>, who helped develop the algorithms. “Without knowing the three-dimensional shape of a protein, it would be like trying to solve that puzzle with a blindfold on.”</p> <p>The ability to determine the 3D atomic structure of protein molecules is critical in understanding how they work and how they will respond to drug therapies, notes Punjani.</p> <p>Drugs work by binding to a specific protein molecule and changing its 3D shape, altering the way it works once inside the body. The ideal drug is designed in a shape that will only bind to a specific protein or proteins involved in a disease while eliminating side effects that occur when drugs bind to other proteins in the body.</p> <p><iframe allowfullscreen frameborder="0" height="500" src="https://www.youtube.com/embed/A3RMkN4hyxw" width="750"></iframe></p> <p>At the same time, researcher&nbsp;<strong>Jana Broecker</strong>&nbsp;and colleagues in the Ernst lab in U of T’s department of biochemistry have discovered a new way to obtain membrane-protein structures. Their research, to be published tomorrow on the cover of the journal&nbsp;<em>Structure</em>, should drastically speed up the discovery of new protein structures&nbsp;– thus also contributing to the development of new and better drugs.</p> <p>In Punjani's research, the&nbsp;new set of algorithms reconstructs 3D structures of protein molecules using microscopic images. Since proteins are tiny – even smaller than a wavelength of light – they can’t be seen directly without using sophisticated techniques like electron cryomicroscopy (cryo-EM). This new method is revolutionizing the way scientists can discover 3D protein structures, allowing the study of many proteins that simply could not be studied in the past.</p> <p>Cryo-EM is unique because it uses high-power microscopes to take tens of thousands of low-resolution images of a frozen protein sample from different positions. The computational problem is to then piece together the correct high-resolution 3D structure from the low-resolution 2D images.</p> <p>“Our approach solves some of the major problems in terms of speed and number of structures you can determine,” says Professor <strong>David Fleet,</strong> chair of the computer and mathematical sciences department at U of T Scarborough and Punjani’s PhD supervisor.&nbsp;&nbsp;</p> <p>The algorithms, which were co-developed by Fleet’s former post-doctoral researcher <strong>Marcus Brubaker</strong>, now an assistant professor at York University, could significantly aid in the development of new drugs because they provide a faster, more efficient means at arriving at the correct protein structure.&nbsp;</p> <p>“Existing techniques take several days or even weeks to generate a 3D structure on a cluster of computers,” says Brubaker. “Our approach can make it possible in minutes on a single computer.”</p> <p>Punjani adds that existing techniques often generate incorrect structures unless the user provides an accurate guess of the molecule being studied. What’s novel about this&nbsp;approach is that it eliminates the need for prior knowledge about the protein molecule being studied.</p> <p>“We hope this will allow discoveries to happen at a ground-breaking pace in structural biology,” says Punjani. “The ultimate goal is that it will directly lead to new drug candidates for diseases, and a much deeper understanding of how life works at the atomic level.”</p> <p>The research, which included a collaboration with U of T Professor <strong>John Rubinstein</strong>, a Canada Research Chair in Electron Cryomicroscopy, received funding from the Natural Sciences and Engineering Research Council of Canada (NSERC). It’s also been published in the current edition of the journal <a href="http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4169.html"><em>Nature Methods</em></a>.</p> <p>Meanwhile, the team’s startup, Structura Biotechnology Inc., has developed the algorithms into a new cryo-EM platform called cryoSPARC that is already being used in labs across North America.</p> <p>The startup has received funding and support from U of T’s Innovations and Partnership’s Office (IPO) through the Connaught Innovation Award, U of T’s Early Stage Technologies (UTEST) program, the Ontario Centres of Excellence (OCE)&nbsp;and FedDev Ontario’s Investing in Commercialization Partnerships program with York University.</p> </div> <div class="field field--name-field-news-home-page-banner field--type-boolean field--label-above"> <div class="field__label">News home page banner</div> <div class="field__item">Off</div> </div> Mon, 06 Feb 2017 16:14:36 +0000 ullahnor 104591 at Xmas gift from U of T research: the algorithm behind perfect wine and cheese pairings /news/xmas-gift-u-t-research-algorithm-behind-perfect-wine-and-cheese-pairings <span class="field field--name-title field--type-string field--label-hidden">Xmas gift from U of T research: the algorithm behind perfect wine and cheese pairings</span> <div class="field field--name-field-featured-picture field--type-image field--label-hidden field__item"> <img loading="eager" srcset="/sites/default/files/styles/news_banner_370/public/2016-12-05-wine-and-cheese-lead.jpg?h=fab47044&amp;itok=o3NgT6qf 370w, /sites/default/files/styles/news_banner_740/public/2016-12-05-wine-and-cheese-lead.jpg?h=fab47044&amp;itok=5M9brSLq 740w, /sites/default/files/styles/news_banner_1110/public/2016-12-05-wine-and-cheese-lead.jpg?h=fab47044&amp;itok=fWsu1pA- 1110w" sizes="(min-width:1200px) 1110px, (max-width: 1199px) 80vw, (max-width: 767px) 90vw, (max-width: 575px) 95vw" width="740" height="494" src="/sites/default/files/styles/news_banner_370/public/2016-12-05-wine-and-cheese-lead.jpg?h=fab47044&amp;itok=o3NgT6qf" alt="Photo of wine and cheese"> </div> <span class="field field--name-uid field--type-entity-reference field--label-hidden"><span>ullahnor</span></span> <span class="field field--name-created field--type-created field--label-hidden"><time datetime="2016-12-05T12:11:13-05:00" title="Monday, December 5, 2016 - 12:11" class="datetime">Mon, 12/05/2016 - 12:11</time> </span> <div class="clearfix text-formatted field field--name-field-cutline-long field--type-text-long field--label-above"> <div class="field__label">Cutline</div> <div class="field__item"> (photo by fran.trudeau via Flickr)</div> </div> <div class="field field--name-field-author-reporters field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/news/authors-reporters/jovana-drinjakovic" hreflang="en">Jovana Drinjakovic</a></div> </div> <div class="field field--name-field-author-legacy field--type-string field--label-above"> <div class="field__label">Author legacy</div> <div class="field__item">Jovana Drinjakovic</div> </div> <div class="field field--name-field-topic field--type-entity-reference field--label-above"> <div class="field__label">Topic</div> <div class="field__item"><a href="/news/topics/global-lens" hreflang="en">Global Lens</a></div> </div> <div class="field field--name-field-story-tags field--type-entity-reference field--label-hidden field__items"> <div class="field__item"><a href="/news/tags/artificial-intelligence" hreflang="en">Artificial Intelligence</a></div> <div class="field__item"><a href="/news/tags/algorithm" hreflang="en">Algorithm</a></div> <div class="field__item"><a href="/news/tags/computer-science" hreflang="en">Computer Science</a></div> <div class="field__item"><a href="/news/tags/molecular-genetics" hreflang="en">Molecular Genetics</a></div> <div class="field__item"><a href="/news/tags/donnelly-centre" hreflang="en">Donnelly Centre</a></div> <div class="field__item"><a href="/news/tags/faculty-arts-science" hreflang="en">Faculty of Arts &amp; Science</a></div> <div class="field__item"><a href="/news/tags/faculty-medicine" hreflang="en">Faculty of Medicine</a></div> </div> <div class="clearfix text-formatted field field--name-body field--type-text-with-summary field--label-hidden field__item"><p>Know your Gruyere from Beaufort? And should it come with a splash of Tuscan Sangiovese or Syrah? Don’t panic. This app will turn you into a bon vivant just in time for the holidays!</p> <p><a href="/news/decoding-deluge-data"><strong>Gary Bader</strong></a>, a professor at U of T's Donnelly Centre for Cellular and Biomolecular Research, and his colleagues have created an app that helps folks&nbsp;pair wine with just the right cheese, and vice versa.</p> <p>Bader, who is affiliated with&nbsp;the departments of molecular genetics and computer science in the Faculty of Arts &amp; Science, is also an associate member of Sinai Health’s Lunenfeld-Tanenbaum Research Institute.</p> <p>He is also a member of U of T's cancer-fighting Dream Team.</p> <h3><a href="/news/u-t-researchers-lead-cancer-fighting-dream-team">Read more about the Dream Team</a></h3> <p>The&nbsp;new app caught the eye of&nbsp;<em>The Washington Post. </em>The paper&nbsp;reports that the researchers used wine and cheese pairings as a testing ground for their algorithm called <a href="http://js.cytoscape.org/">Cytoscape</a>, which they developed to map out relationships between genes and proteins in the cell.&nbsp;</p> <p>Bader told the paper&nbsp;that he uses the app&nbsp;when he goes shopping for cheese, and that he has “gotten a lot of mileage out of it at parties.”&nbsp;</p> <h3><a href="https://www.washingtonpost.com/news/wonk/wp/2016/12/03/how-to-throw-the-ultimate-wine-and-cheese-party-using-the-miracle-of-data/?utm_term=.b8a47066b76f">Read <em>The Washington Post </em>story</a></h3> </div> <div class="field field--name-field-news-home-page-banner field--type-boolean field--label-above"> <div class="field__label">News home page banner</div> <div class="field__item">Off</div> </div> Mon, 05 Dec 2016 17:11:13 +0000 ullahnor 102701 at