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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>
	<lastBuildDate>Fri, 27 Aug 2010 14:08:33 +0000</lastBuildDate>
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		<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>
		</item>
		<item>
		<title>CAPRI or: What is the State of Protein-Protein Docking?</title>
		<link>http://rosettadesigngroup.com/blog/535/capri-state-of-protein-protein-docking/</link>
		<comments>http://rosettadesigngroup.com/blog/535/capri-state-of-protein-protein-docking/#comments</comments>
		<pubDate>Mon, 11 Jan 2010 19:52:26 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Events]]></category>
		<category><![CDATA[Weird science]]></category>
		<category><![CDATA[CAPRI]]></category>
		<category><![CDATA[CASP]]></category>
		<category><![CDATA[Evaluation]]></category>
		<category><![CDATA[Meeting]]></category>
		<category><![CDATA[Protein-Protein Docking]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=535</guid>
		<description><![CDATA[This is the first post in a series, summarizing the CAPRI (Critical Assessment of PRediction of Interactions) 4th Evaluation meeting. In this post I'll try to give a more personal perspective of the experiment results, the state and trends of computational protein-protein docking and the vibes behind the scenes. The next posts in the series will shortly summarize select talks from the meeting, kindly provided by the speakers.]]></description>
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		<slash:comments>2</slash:comments>
		</item>
		<item>
		<title>How to detect a forged PDB</title>
		<link>http://rosettadesigngroup.com/blog/526/how-to-detect-a-forged-pdb/</link>
		<comments>http://rosettadesigngroup.com/blog/526/how-to-detect-a-forged-pdb/#comments</comments>
		<pubDate>Sat, 02 Jan 2010 10:54:10 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[News]]></category>
		<category><![CDATA[Weird science]]></category>
		<category><![CDATA[1BEF]]></category>
		<category><![CDATA[forged]]></category>
		<category><![CDATA[Gerard Kleywegt]]></category>
		<category><![CDATA[MolProbity]]></category>
		<category><![CDATA[pdb]]></category>
		<category><![CDATA[PROCHECK]]></category>
		<category><![CDATA[RosettaHoles]]></category>
		<category><![CDATA[StructureGate]]></category>
		<category><![CDATA[Validation]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=526</guid>
		<description><![CDATA[Most of you probably heard about the recent retraction of some 12 structures (1BEF, 1CMW, 1DF9/2QID, 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0) from the PDB. Reported first by The University of Alabama at Birmingham and follwing by structural biology blogs as p212121 and ByteSizeBio - also known as "Structuregate". One question that arises is - was this preventable?]]></description>
		<wfw:commentRss>http://rosettadesigngroup.com/blog/526/how-to-detect-a-forged-pdb/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Interactive 3D Molecules in articles</title>
		<link>http://rosettadesigngroup.com/blog/448/interactive-3d-molecules-in-articles/</link>
		<comments>http://rosettadesigngroup.com/blog/448/interactive-3d-molecules-in-articles/#comments</comments>
		<pubDate>Sat, 24 Oct 2009 08:29:47 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Weird science]]></category>
		<category><![CDATA[3D animation]]></category>
		<category><![CDATA[PLoS ONE]]></category>
		<category><![CDATA[Proteopedia]]></category>
		<category><![CDATA[SGC]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=448</guid>
		<description><![CDATA[PLoS ONE launched a new collection titled “Structural Biology and Human Health: Medically Relevant Proteins from the SGC” which makes use of three dimensional molecular animation technology.]]></description>
		<wfw:commentRss>http://rosettadesigngroup.com/blog/448/interactive-3d-molecules-in-articles/feed/</wfw:commentRss>
		<slash:comments>3</slash:comments>
		</item>
		<item>
		<title>M2 quiz: select the correct adamantane binding model.</title>
		<link>http://rosettadesigngroup.com/blog/407/correct-adamantane-binding-model/</link>
		<comments>http://rosettadesigngroup.com/blog/407/correct-adamantane-binding-model/#comments</comments>
		<pubDate>Tue, 02 Jun 2009 17:55:28 +0000</pubDate>
		<dc:creator>admin</dc:creator>
				<category><![CDATA[Literature Reviews]]></category>
		<category><![CDATA[Weird science]]></category>
		<category><![CDATA[Adamantane]]></category>
		<category><![CDATA[Discount Thoughts]]></category>
		<category><![CDATA[Infulenza]]></category>
		<category><![CDATA[M2]]></category>
		<category><![CDATA[Rimantadine]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=407</guid>
		<description><![CDATA[Adamantane drugs inhibit the M2 proton channel from influenza A, a tiny tetrameric protein that equalizes pH between the virus and the endosome of the cell that has swallowed it. Over the past few years a great deal of structural evidence has accumulated showing how adamantane drugs work. Problem is that the evidence supports two different models of M2 inhibition. "Discount Thoughts" provides a great review on a mechanism that is truly a tough nut to crack.]]></description>
		<wfw:commentRss>http://rosettadesigngroup.com/blog/407/correct-adamantane-binding-model/feed/</wfw:commentRss>
		<slash:comments>2</slash:comments>
		</item>
		<item>
		<title>SCWRL4.0 Released. Any Questions?</title>
		<link>http://rosettadesigngroup.com/blog/403/scwrl40-released-any-questions/</link>
		<comments>http://rosettadesigngroup.com/blog/403/scwrl40-released-any-questions/#comments</comments>
		<pubDate>Mon, 25 May 2009 16:17:22 +0000</pubDate>
		<dc:creator>admin</dc:creator>
				<category><![CDATA[Resources]]></category>
		<category><![CDATA[Weird science]]></category>
		<category><![CDATA[Roland Dunbrack]]></category>
		<category><![CDATA[rotamer library]]></category>
		<category><![CDATA[SCWRL]]></category>
		<category><![CDATA[side chain modeling]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=403</guid>
		<description><![CDATA[Roland Dunbrack shows off the capabilities of SCWRL4, the new version of his famous side chain prediction software. Indeed it seems that the new version has come a long way, especially in the form of a new, smoother backbone-dependent rotamer library. Roland promises to answer any questions regarding the new rotamer library, SCWRL, and also random questions.]]></description>
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		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Molecular Dynamics Vs. Monte Carlo</title>
		<link>http://rosettadesigngroup.com/blog/400/molecular-dynamics-vs-monte-carlo/</link>
		<comments>http://rosettadesigngroup.com/blog/400/molecular-dynamics-vs-monte-carlo/#comments</comments>
		<pubDate>Sun, 24 May 2009 18:29:08 +0000</pubDate>
		<dc:creator>admin</dc:creator>
				<category><![CDATA[Weird science]]></category>
		<category><![CDATA[Bosco Ho]]></category>
		<category><![CDATA[Computation time]]></category>
		<category><![CDATA[CONCORD]]></category>
		<category><![CDATA[DESMOND]]></category>
		<category><![CDATA[Molecular Dynamics]]></category>
		<category><![CDATA[Monte Carlo Simulations]]></category>
		<category><![CDATA[NMR]]></category>
		<category><![CDATA[Protein Dynamics]]></category>
		<category><![CDATA[RDC]]></category>
		<category><![CDATA[S order parameter]]></category>
		<category><![CDATA[Ubiquitin]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=400</guid>
		<description><![CDATA[I'm happy to cross-post another elegant piece written by the MD specialist Bosco Ho. In this post Bosco compares the performance of Molecular Dynamics simulations with Monte Carlo simulations in reconstructing NMR S order parameters for microsecond biological processes. Curious to know which is better ?]]></description>
		<wfw:commentRss>http://rosettadesigngroup.com/blog/400/molecular-dynamics-vs-monte-carlo/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Scientific Wikis &#8211; Part I</title>
		<link>http://rosettadesigngroup.com/blog/373/scientific-wikis-part-i/</link>
		<comments>http://rosettadesigngroup.com/blog/373/scientific-wikis-part-i/#comments</comments>
		<pubDate>Mon, 11 May 2009 14:50:59 +0000</pubDate>
		<dc:creator>admin</dc:creator>
				<category><![CDATA[Resources]]></category>
		<category><![CDATA[Weird science]]></category>
		<category><![CDATA[Colaboration]]></category>
		<category><![CDATA[Dan Bolser]]></category>
		<category><![CDATA[Jong Bhak]]></category>
		<category><![CDATA[MetaBase]]></category>
		<category><![CDATA[PDBwiki]]></category>
		<category><![CDATA[Wiki]]></category>
		<category><![CDATA[Wikipedia]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=373</guid>
		<description><![CDATA[Are wikis the future of scientific collaboration in biology? 

The tremendous success of Wikipedia has raised the possibility of using wiki technology for scientific collaboration. However, it is not yet clear if traditional scientific methods can be acceptably incorporated into the 'wiki' paradigm. Despite this uncertainty, many tens of 'scientific-wikis' currently exist [1], with many more 'annotation-wikis' on the horizon. In this post we will discuss two key scientific concepts, and try to assess how they fit (or not) within the 'wiki' model. By Dan Bolser and Jong Bhak.]]></description>
		<wfw:commentRss>http://rosettadesigngroup.com/blog/373/scientific-wikis-part-i/feed/</wfw:commentRss>
		<slash:comments>3</slash:comments>
		</item>
		<item>
		<title>Macromolecular Modeling for Molecular Systems Engineering</title>
		<link>http://rosettadesigngroup.com/blog/344/macromolecular-modeling-molecular-systems-engineering/</link>
		<comments>http://rosettadesigngroup.com/blog/344/macromolecular-modeling-molecular-systems-engineering/#comments</comments>
		<pubDate>Thu, 16 Apr 2009 14:16:14 +0000</pubDate>
		<dc:creator>admin</dc:creator>
				<category><![CDATA[Weird science]]></category>
		<category><![CDATA[Eric Drexler]]></category>
		<category><![CDATA[Guest]]></category>
		<category><![CDATA[Macromolecular modeling]]></category>
		<category><![CDATA[Molecular Systems Engineering]]></category>
		<category><![CDATA[Nanotechnology]]></category>
		<category><![CDATA[Protein design]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=344</guid>
		<description><![CDATA[Macromolecular systems engineering can help us meet some of the most important technological challenges in the world today, ranging from medicine to renewable energy, and the development of better-integrated computational design tools will accelerate progress. Macromolecular modeling capabilities are advancing rapidly, but much of their potential for supporting systems engineering has yet to be exploited. In this post, I’d like to describe the fundamental nature of the problems and outline some of what needs to be done to make their potential a reality. By Dr. Eric Drexler.]]></description>
		<wfw:commentRss>http://rosettadesigngroup.com/blog/344/macromolecular-modeling-molecular-systems-engineering/feed/</wfw:commentRss>
		<slash:comments>4</slash:comments>
		</item>
		<item>
		<title>Protein-Protein Docking on the rise.</title>
		<link>http://rosettadesigngroup.com/blog/314/protein-protein-docking-on-the-rise/</link>
		<comments>http://rosettadesigngroup.com/blog/314/protein-protein-docking-on-the-rise/#comments</comments>
		<pubDate>Mon, 30 Mar 2009 14:53:02 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Polls]]></category>
		<category><![CDATA[Weird science]]></category>
		<category><![CDATA[Protein-Protein Docking]]></category>
		<category><![CDATA[Rosetta]]></category>
		<category><![CDATA[RosettaDock]]></category>
		<category><![CDATA[Trends]]></category>
		<category><![CDATA[webinar]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=314</guid>
		<description><![CDATA[We have recently conducted a poll amongst people interested in learning more about the Rosetta software (as a preliminary step to the Rosetta Academic Training Workshop). One of the questions in that poll was: "Which Rosetta related topics is of the most interest to you?" The results (from ~200 participants) are summarized in the graph below.]]></description>
		<wfw:commentRss>http://rosettadesigngroup.com/blog/314/protein-protein-docking-on-the-rise/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
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