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	<title>Macromolecular Modeling Blog ™ &#187; Literature Reviews</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>
	<lastBuildDate>Wed, 14 Dec 2011 15:12:49 +0000</lastBuildDate>
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		<title>A twitter roundup</title>
		<link>http://rosettadesigngroup.com/blog/916/twitter-roundup/</link>
		<comments>http://rosettadesigngroup.com/blog/916/twitter-roundup/#comments</comments>
		<pubDate>Sat, 05 Nov 2011 15:25:28 +0000</pubDate>
		<dc:creator>admin</dc:creator>
				<category><![CDATA[Resources]]></category>
		<category><![CDATA[Title Madness]]></category>
		<category><![CDATA[links]]></category>
		<category><![CDATA[Twitter]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=916</guid>
		<description><![CDATA[For those not yet following us (@molmodelblog) on twitter, a roundup of interesting links from the weekend: MIT Research: New Protein Folding Model Helps With Genetic Data Deluge http://bit.ly/rwsl0u Postdoctoral Position in Protein Engineering and Chemical Biology, The Eindhoven University of Technology, Netherlandshttp://bit.ly/rPbWIT Tau proteins in nerve cells interact strongly with neg. lipids on the membrane [...]]]></description>
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		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>One Sided De-Novo Computational Design of a Protein-Protein Interaction</title>
		<link>http://rosettadesigngroup.com/blog/874/one-sided-de-novo-computational-design-protein-protein-interaction/</link>
		<comments>http://rosettadesigngroup.com/blog/874/one-sided-de-novo-computational-design-protein-protein-interaction/#comments</comments>
		<pubDate>Wed, 08 Jun 2011 16:09:46 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Interviews]]></category>
		<category><![CDATA[Literature Reviews]]></category>
		<category><![CDATA[Computational Design]]></category>
		<category><![CDATA[david baker]]></category>
		<category><![CDATA[Hemaglutinin]]></category>
		<category><![CDATA[interface design]]></category>
		<category><![CDATA[protein-protein interactions]]></category>
		<category><![CDATA[Rosetta]]></category>
		<category><![CDATA[Sarel Fleishman]]></category>
		<category><![CDATA[Science]]></category>
		<category><![CDATA[specificity]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=874</guid>
		<description><![CDATA[In a recent Science paper, Sarel Fleishman et al. report the de-novo computational design of a protein interface to specifically target and tightly bind a surface patch of the flu hemaglutinin protein. We interview Sarel to get the insights from behind the scenes and the outlook for this exciting approach. ]]></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>A more dynamic literature review</title>
		<link>http://rosettadesigngroup.com/blog/853/a-more-dynamic-literature-review/</link>
		<comments>http://rosettadesigngroup.com/blog/853/a-more-dynamic-literature-review/#comments</comments>
		<pubDate>Thu, 19 May 2011 17:39:53 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Literature Reviews]]></category>
		<category><![CDATA[Title Madness]]></category>
		<category><![CDATA[Disqus]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=853</guid>
		<description><![CDATA[Though I like posting them, and some of the readers like sifting through, the literature reviews always struck me as too static, I wanted to have a more nimble system that can allow readers to comment on a specific paper, to 'like' specific papers, and to be able to sort the list this way or another. Following the recent post on Annotator, it came to mind that Disqus might indeed be the answer for a few of these problems.]]></description>
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		<slash:comments>85</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>Concerted Dynamics Link Allosteric Sites in the PBX Homeodomain</title>
		<link>http://rosettadesigngroup.com/blog/822/dynamics-link-allosterics-of-homeodomain/</link>
		<comments>http://rosettadesigngroup.com/blog/822/dynamics-link-allosterics-of-homeodomain/#comments</comments>
		<pubDate>Tue, 21 Dec 2010 21:10:20 +0000</pubDate>
		<dc:creator>admin</dc:creator>
				<category><![CDATA[Literature Reviews]]></category>
		<category><![CDATA[Allostery]]></category>
		<category><![CDATA[Conformational Sampling]]></category>
		<category><![CDATA[Conformational Selection]]></category>
		<category><![CDATA[Discount Thoughts]]></category>
		<category><![CDATA[Homeodomain]]></category>
		<category><![CDATA[NMR]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=822</guid>
		<description><![CDATA[In a recent post in "Discount Thoughts" Michael Clarkson reviews a paper examining the dynamics of allostery in PBX1 homeodomain. Another example for a possible conformational selection binding mechanism.]]></description>
		<wfw:commentRss>http://rosettadesigngroup.com/blog/822/dynamics-link-allosterics-of-homeodomain/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Literature Review &#8211; Nov.(+Oct.) 2010</title>
		<link>http://rosettadesigngroup.com/blog/793/literature-review-nov-oct-2010/</link>
		<comments>http://rosettadesigngroup.com/blog/793/literature-review-nov-oct-2010/#comments</comments>
		<pubDate>Thu, 25 Nov 2010 18:15:57 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Literature Reviews]]></category>
		<category><![CDATA[Title Madness]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=793</guid>
		<description><![CDATA[As usual, a long absence means two things, lots of work to do, and lots of papers to read. You can find here our pickings from the recent literature. Enjoy.]]></description>
		<wfw:commentRss>http://rosettadesigngroup.com/blog/793/literature-review-nov-oct-2010/feed/</wfw:commentRss>
		<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>
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