Unfolding the mystery of proteins

<script src="http://static.meteorsolutions.com/metsol.js" type="text/javascript"></script><script src="http://cdnt.meteorsolutions.com/api/multi_track?application_id=6787616a-bec6-48d3-8b3c-0f08ab2bf44a&url_storage_source=hash&query_string_tag_key=mtag&query_string_tag_key=source&query_string_tag_key=src" type="text/javascript"></script><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;">U.S. Patent #8,423,339: Visual analysis of a protein folding process </span></span><br /><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;">Patent Issued: April 16, 2013</span></span><br /><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;">Inventors: <a href="http://researcher.ibm.com/researcher/view.php?person=us-parida">Laxmi Parida</a>, <a href="http://researcher.ibm.com/researcher/view.php?person=us-ruhongz">Ruhong Zhou</a></span></span><br /><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><br /></span></span><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><i>What is patent #8,423,339? By Laxmi Parida, Manager, IBM Computational Genomics Group.</i></span></span><br /><br /><div class="separator" style="clear: both; text-align: center;"><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQ9kyDQqm3XQRykzWCQvgcuF6QfYTD5JCZ3a9PcxZCtWwwp7sjIQIi_HcCZHwhdm90Vq1d3glwR6jVoTXO_9Q19U8v8AJsQGuFTiRUgZpFW2HX_stsEf1KVU7qYISe-g23LqXCi5RP6_M/s1600/laxmi_parida.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgQ9kyDQqm3XQRykzWCQvgcuF6QfYTD5JCZ3a9PcxZCtWwwp7sjIQIi_HcCZHwhdm90Vq1d3glwR6jVoTXO_9Q19U8v8AJsQGuFTiRUgZpFW2HX_stsEf1KVU7qYISe-g23LqXCi5RP6_M/s1600/laxmi_parida.jpg" /></a></span></span></div><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;">Proteins do just about everything in our cells. And those functions, from hormones transport to muscle contraction and much more, are determined by the order and arrangement of protein building blocks, amino acids. <a href="http://patft.uspto.gov/netacgi/nph-Parser?Sect1=PTO1&Sect2=HITOFF&d=PALL&p=1&u=%2Fnetahtml%2FPTO%2Fsrchnum.htm&r=1&f=G&l=50&s1=8,423,339.PN.&OS=PN/8,423,339&RS=PN/8,423,339">Patent #8,423,339</a> gives scientists a way to break down that folding process – which happens in the fraction of a blink of an eye – to understand why proteins fold (and mis-fold) into certain shapes.</span></span><br /><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><br /></span></span><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;">In nature, amino acids in a cell bind together and form a specifically shaped protein. How does this happen? We’re still trying to figure that out. It even has its own paradox, <a href="http://en.wikipedia.org/wiki/Levinthal%27s_paradox">Levinthal’s Paradox</a>, stating that the folding can’t be random (even though it seems that way) because it’s too complicated. </span></span><br /><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><br /></span></span><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;">We know what proteins are made of, but since we can’t see how proteins fold in nature, we have to simulate them. And we’ve been simulating protein folding since before <a href="http://www-03.ibm.com/ibm/history/ibm100/us/en/icons/bluegene/">Blue Gene/L in 1999</a>. Our patent uses the data from these simulations to find and understand the paths the amino acids take during the folding process. </span></span><br /><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><br /></span></span><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;">The tough thing about finding patterns in the process of protein folding is that everything in the data could potentially be a pattern. So, we have to hunt for informative combinations of values that surface again and again – not necessarily in tandem, in the process of folding.</span></span><br /><br /><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody><tr><td style="text-align: center;"><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg2hdXrgPmR3i1xOzQZmylxLOeuCIMWHgwLJ7farbAZO4ubQ2ULYVQkRXeOCRDNnuhcwKivM7BbNm9JBhq7qfFiIAJhA0M8bKGZQqBzmh7GPBdEsK0gRlVjiC0cQZmDNlW_Y9Tq1Fy0S98/s1600/PROTERAN2.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg2hdXrgPmR3i1xOzQZmylxLOeuCIMWHgwLJ7farbAZO4ubQ2ULYVQkRXeOCRDNnuhcwKivM7BbNm9JBhq7qfFiIAJhA0M8bKGZQqBzmh7GPBdEsK0gRlVjiC0cQZmDNlW_Y9Tq1Fy0S98/s1600/PROTERAN2.jpg" width="400" /></a></span></span></td></tr><tr><td class="tr-caption" style="text-align: center;"><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;">Visualization of the varying landscape of patterns as a protein folds</span></span></td></tr></tbody></table><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><br /></span></span><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;">These simulations that create 3D models generate massive amounts of data. But our pattern discovery technique works at the level of the simulator, from workstation to supercomputer. It efficiently combs the data to find these invariant combinatorial subsets, which could provide valuable insight into the folding process. </span></span><br /><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><br /></span></span><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;">Knowing how proteins fold or why they mis-fold will help us understand how cells work and don’t work. Say, in the case of <a href="http://en.wikipedia.org/wiki/Bovine_spongiform_encephalopathy">bovine spongiform encephalopathy</a> (mad cow disease). By understanding the process that created the mis-shapen prion, we could possibly cure or eradicate it, or any other such disease. </span></span><br /><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;"><br /></span></span><span style="font-family: Arial,Helvetica,sans-serif;"><span style="font-size: small;">IBM has led in total U.S. patents for 21 year in a row in 2013. Read more about patents like #8,423,339, <a href="http://www-03.ibm.com/press/us/en/presskit/42874.wss">here</a>.</span></span>

bluegene invention patent protein folding Unfolding the mystery of proteins

U.S. Patent #8,423,339: Visual analysis of a protein folding process Patent Issued: April 16, 2013 Inventors: Laxmi Parida , Ruhong Zhou Wha...

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