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	<title>Macromolecular Modeling Blog ™ &#187; Weird science</title>
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	<link>http://rosettadesigngroup.com/blog</link>
	<description>Trading tips and news on modeling proteins, DNA, RNA, small molecules, folding, docking, design.....</description>
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		<title>Protein design: breaks gluten, wins iGEM2011</title>
		<link>http://rosettadesigngroup.com/blog/921/protein-design-breaks-gluten-wins-igem2011/</link>
		<comments>http://rosettadesigngroup.com/blog/921/protein-design-breaks-gluten-wins-igem2011/#comments</comments>
		<pubDate>Wed, 09 Nov 2011 14:47:02 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[News]]></category>
		<category><![CDATA[Weird science]]></category>
		<category><![CDATA[Diesel]]></category>
		<category><![CDATA[FoldIt]]></category>
		<category><![CDATA[Gluten]]></category>
		<category><![CDATA[iGEM]]></category>
		<category><![CDATA[Protein design]]></category>
		<category><![CDATA[Rosetta]]></category>
		<category><![CDATA[UW]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=921</guid>
		<description><![CDATA[An undergraduate group of students from the University of Washington, managed to redesign an enzyme to efficiently break down a model peptide for Gluten, achieving an increase in activity of hundreds fold over the only current clinically tested treatment for Gluten intolerance - Winning iGEM2011. All this, over the summer. Oh, and they also managed to produce Diesel in E. Coli.]]></description>
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		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Olympic Crystal Packing</title>
		<link>http://rosettadesigngroup.com/blog/894/olympic-crystal-packing/</link>
		<comments>http://rosettadesigngroup.com/blog/894/olympic-crystal-packing/#comments</comments>
		<pubDate>Fri, 04 Nov 2011 06:39:50 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Weird science]]></category>
		<category><![CDATA[Crystal Packing]]></category>
		<category><![CDATA[Crystallography]]></category>
		<category><![CDATA[Olympic]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=894</guid>
		<description><![CDATA[In the spirit of the 2012 Olympic games. Found at the webpage of the group of Prof. Heinz Neumann, Department for Molecular Structural Biology, Georg-August-University Göttingen. Anyone knows what protein is it? HT to ravehb for the finding. Related postsThe Europeans are cleaning up the PDB, woohoo!!!Short Course: Crystallography for Modelers]]></description>
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		<slash:comments>1</slash:comments>
		</item>
		<item>
		<title>A PLoS ONE Rosetta Collection</title>
		<link>http://rosettadesigngroup.com/blog/865/a-plos-one-rosetta-collection/</link>
		<comments>http://rosettadesigngroup.com/blog/865/a-plos-one-rosetta-collection/#comments</comments>
		<pubDate>Thu, 26 May 2011 18:07:57 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Literature Reviews]]></category>
		<category><![CDATA[News]]></category>
		<category><![CDATA[Weird science]]></category>
		<category><![CDATA[Enzyme Design]]></category>
		<category><![CDATA[FlexPepDock]]></category>
		<category><![CDATA[Puzzels]]></category>
		<category><![CDATA[Rosetta]]></category>
		<category><![CDATA[RosettaCon]]></category>
		<category><![CDATA[RosettaCon 2011]]></category>
		<category><![CDATA[RosettaCon11]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=865</guid>
		<description><![CDATA[Three articles recently published in PLoS ONE are the harbinger of a RosettaCon 2010 PLoS one collection. How do you design a new enzyme from scratch? How do you model peptide binding with almost no prior information? And what puzzles CAN'T Rosetta solve?]]></description>
		<wfw:commentRss>http://rosettadesigngroup.com/blog/865/a-plos-one-rosetta-collection/feed/</wfw:commentRss>
		<slash:comments>2</slash:comments>
		</item>
		<item>
		<title>Annotatr and The MD Club</title>
		<link>http://rosettadesigngroup.com/blog/846/annotatr-and-the-md-club/</link>
		<comments>http://rosettadesigngroup.com/blog/846/annotatr-and-the-md-club/#comments</comments>
		<pubDate>Fri, 06 May 2011 12:02:37 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Literature Reviews]]></category>
		<category><![CDATA[Resources]]></category>
		<category><![CDATA[Weird science]]></category>
		<category><![CDATA[Annotatr]]></category>
		<category><![CDATA[Bosco Ho]]></category>
		<category><![CDATA[CiteULike]]></category>
		<category><![CDATA[Disqus]]></category>
		<category><![CDATA[Journal Club]]></category>
		<category><![CDATA[MD]]></category>
		<category><![CDATA[Molecular Dynamics]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=846</guid>
		<description><![CDATA[Some months ago, Bosco Ho, Molecular Dynamics (MD) boy wonder and HTML5 wiz, contacted a group of scientists, myself included, to start a world wide Journal Club (JC). The subject: Molecular Dynamics, the venue? Annotatr - a mashup of CiteULike and Disqus. The motivation behind Annotatr was to get scientists to comment on articles (lower the energy barrier if you prefer).

Since then the MD JC had several prolific sessions, discussing some great MD papers on which I'll discuss briefly below.]]></description>
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		<slash:comments>2</slash:comments>
		</item>
		<item>
		<title>Use of Molecular Vision in Education</title>
		<link>http://rosettadesigngroup.com/blog/789/molecular-vision-in-education/</link>
		<comments>http://rosettadesigngroup.com/blog/789/molecular-vision-in-education/#comments</comments>
		<pubDate>Sat, 09 Oct 2010 15:11:27 +0000</pubDate>
		<dc:creator>admin</dc:creator>
				<category><![CDATA[Polls]]></category>
		<category><![CDATA[Weird science]]></category>
		<category><![CDATA[education]]></category>
		<category><![CDATA[molecular viewer]]></category>
		<category><![CDATA[Molecular Vision]]></category>
		<category><![CDATA[poll]]></category>
		<category><![CDATA[survey]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=789</guid>
		<description><![CDATA[Bob Bateman* and Paul Craig** recently wrote an article entitled, &#8220;A Proficiency Rubric for Biomacromolecular 3D Literacy&#8220;, for the Education Corner of the PDB newsletter, where they presented three levels of 3D biomolecular literacy: Introductory Biology (novice level), Biochemistry/Cell Biology (amateur level) and Structural Biology Graduate Student (expert level). Together with Lea Michel** their goal [...]]]></description>
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		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Deriving Inhibitory Peptides from Globular Protein–Protein Interactions</title>
		<link>http://rosettadesigngroup.com/blog/769/derived-inhibitory-peptides/</link>
		<comments>http://rosettadesigngroup.com/blog/769/derived-inhibitory-peptides/#comments</comments>
		<pubDate>Tue, 28 Sep 2010 13:41:07 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Literature Reviews]]></category>
		<category><![CDATA[Weird science]]></category>
		<category><![CDATA[Binding]]></category>
		<category><![CDATA[Ephrin]]></category>
		<category><![CDATA[FlexPepDock]]></category>
		<category><![CDATA[inhibitory peptides]]></category>
		<category><![CDATA[Modeling peptides]]></category>
		<category><![CDATA[peptiDB]]></category>
		<category><![CDATA[Peptide docking]]></category>
		<category><![CDATA[Peptide drugs]]></category>
		<category><![CDATA[Peptide-protein interactions]]></category>
		<category><![CDATA[Peptides]]></category>
		<category><![CDATA[protein-protein interactions]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=769</guid>
		<description><![CDATA[There are several forms of peptide-protein interactions, one of which are globular PPIs mediated by a dominant linear peptide at the interface. To what extent could peptides extracted from a globular protein monomer be used to inhibit the interaction to its partner? In this work, we have investigated the possibility of deriving peptides from the interface of globular proteins to design inhibitors that would compete with their native interaction.]]></description>
		<wfw:commentRss>http://rosettadesigngroup.com/blog/769/derived-inhibitory-peptides/feed/</wfw:commentRss>
		<slash:comments>2</slash:comments>
		</item>
		<item>
		<title>Sub-angstrom modeling of complexes between flexible peptides and globular proteins</title>
		<link>http://rosettadesigngroup.com/blog/748/sub-angstrom-peptide-docking/</link>
		<comments>http://rosettadesigngroup.com/blog/748/sub-angstrom-peptide-docking/#comments</comments>
		<pubDate>Mon, 27 Sep 2010 15:41:32 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Literature Reviews]]></category>
		<category><![CDATA[Weird science]]></category>
		<category><![CDATA[Binding]]></category>
		<category><![CDATA[FlexPepDock]]></category>
		<category><![CDATA[Modeling peptides]]></category>
		<category><![CDATA[Peptide docking]]></category>
		<category><![CDATA[Peptide-protein interactions]]></category>
		<category><![CDATA[Peptides]]></category>
		<category><![CDATA[Rosetta]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=748</guid>
		<description><![CDATA[We present Rosetta FlexPepDock, a novel tool for refining coarse peptide–protein models that allows significant changes in both peptide backbone and side chains. We obtain high resolution models, often of sub-angstrom backbone quality, over an extensive and general benchmark of 89 peptide–protein interactions.]]></description>
		<wfw:commentRss>http://rosettadesigngroup.com/blog/748/sub-angstrom-peptide-docking/feed/</wfw:commentRss>
		<slash:comments>1</slash:comments>
		</item>
		<item>
		<title>The Structural Basis of Peptide-Protein Binding Strategies</title>
		<link>http://rosettadesigngroup.com/blog/742/the-structural-basis-of-peptide-protein-binding-strategies/</link>
		<comments>http://rosettadesigngroup.com/blog/742/the-structural-basis-of-peptide-protein-binding-strategies/#comments</comments>
		<pubDate>Sat, 25 Sep 2010 13:13:17 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Literature Reviews]]></category>
		<category><![CDATA[Weird science]]></category>
		<category><![CDATA[Basic science]]></category>
		<category><![CDATA[Binding]]></category>
		<category><![CDATA[Biophysical]]></category>
		<category><![CDATA[Furman Group]]></category>
		<category><![CDATA[peptiDB]]></category>
		<category><![CDATA[Peptide-protein interactions]]></category>
		<category><![CDATA[Peptides]]></category>
		<category><![CDATA[protein-protein interactions]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=742</guid>
		<description><![CDATA[How can peptides overcome the entropic cost involved in switching from an unstructured, flexible peptide to a rigid, well-defined bound structure? What are the strategies used by peptides in order to bind their protein receptor? How is this different than protein-protein interactions? In this work we performed A structure-based analysis of peptide-protein interactions to try and answer these questions.]]></description>
		<wfw:commentRss>http://rosettadesigngroup.com/blog/742/the-structural-basis-of-peptide-protein-binding-strategies/feed/</wfw:commentRss>
		<slash:comments>4</slash:comments>
		</item>
		<item>
		<title>Introducing Peptide-Protein Interactions</title>
		<link>http://rosettadesigngroup.com/blog/739/introducing-peptide-protein-interactions/</link>
		<comments>http://rosettadesigngroup.com/blog/739/introducing-peptide-protein-interactions/#comments</comments>
		<pubDate>Fri, 24 Sep 2010 12:38:05 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Literature Reviews]]></category>
		<category><![CDATA[Weird science]]></category>
		<category><![CDATA[Furman Group]]></category>
		<category><![CDATA[Peptide drugs]]></category>
		<category><![CDATA[Peptide therapeutics]]></category>
		<category><![CDATA[Peptide-protein interactions]]></category>
		<category><![CDATA[Peptides]]></category>
		<category><![CDATA[Peptides in signaling]]></category>
		<category><![CDATA[review]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=739</guid>
		<description><![CDATA[Peptide-protein interactions are gaining much interest of late. The Furman group have recently published a series of papers on the subject of peptide-protein interactions (disclaimer - these were partly authored by yours truly). In this post I will introduce the subject and the motivation to investigate these interactions and in later posts of this 'mini-series' I will get into more details on this on-going research.]]></description>
		<wfw:commentRss>http://rosettadesigngroup.com/blog/739/introducing-peptide-protein-interactions/feed/</wfw:commentRss>
		<slash:comments>4</slash:comments>
		</item>
		<item>
		<title>Models on the cover</title>
		<link>http://rosettadesigngroup.com/blog/579/models-on-the-cover/</link>
		<comments>http://rosettadesigngroup.com/blog/579/models-on-the-cover/#comments</comments>
		<pubDate>Wed, 10 Feb 2010 19:08:55 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Weird science]]></category>
		<category><![CDATA[Bar Refaeli]]></category>
		<category><![CDATA[cover]]></category>
		<category><![CDATA[Protein-peptide interactions]]></category>
		<category><![CDATA[Sports Illustrated]]></category>
		<category><![CDATA[Structure]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=579</guid>
		<description><![CDATA[In 2009, an israeli model (Bar Refaeli) had gotten the cover of the sports illustrated special swimsuit issue. In 2010, an israeli modeler had gotten the cover of the february issue of "Structure". Indeed it's hard to say which is more sexy. ]]></description>
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		<slash:comments>0</slash:comments>
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