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	<title>Macromolecular Modeling Blog ™ &#187; Polls</title>
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	<description>Trading tips and news on modeling proteins, DNA, RNA, small molecules, folding, docking, design.....</description>
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		<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>
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		<item>
		<title>Is dynamics the missing link for understanding enzyme catalysis?</title>
		<link>http://rosettadesigngroup.com/blog/649/is-dynamics-the-missing-link-for-understanding-enzyme-catalysis/</link>
		<comments>http://rosettadesigngroup.com/blog/649/is-dynamics-the-missing-link-for-understanding-enzyme-catalysis/#comments</comments>
		<pubDate>Wed, 12 May 2010 18:20:52 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Literature Reviews]]></category>
		<category><![CDATA[Polls]]></category>
		<category><![CDATA[Adenylate Kinase]]></category>
		<category><![CDATA[Catalysis]]></category>
		<category><![CDATA[Dynamics]]></category>
		<category><![CDATA[Enzymes]]></category>
		<category><![CDATA[Karplus]]></category>
		<category><![CDATA[Warshel]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=649</guid>
		<description><![CDATA[How do enzymes catalyze reactions? There are countless answers of course, but one answer that has gained much attention and popularity in recent years is - through intrinsic dynamics. Is that so? PNAS recently published a paper by Arieh Warshel entitled: "Enzyme millisecond conformational dynamics do not catalyze the chemical step". Warshel, an avid assailant of the coupling between dynamics and catalysis was met by Martin Karplus, devoted advocate for catalytic dynamics, to engage in a public dispute over the letters section of PNAS. Who do you find more convincing?]]></description>
		<wfw:commentRss>http://rosettadesigngroup.com/blog/649/is-dynamics-the-missing-link-for-understanding-enzyme-catalysis/feed/</wfw:commentRss>
		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>Which is the fairest secondary structure prediction algorithm of them all?</title>
		<link>http://rosettadesigngroup.com/blog/456/fairest-secondary-structure-prediction-algorithm/</link>
		<comments>http://rosettadesigngroup.com/blog/456/fairest-secondary-structure-prediction-algorithm/#comments</comments>
		<pubDate>Fri, 30 Oct 2009 21:26:15 +0000</pubDate>
		<dc:creator>Xavier Ambroggio</dc:creator>
				<category><![CDATA[Polls]]></category>
		<category><![CDATA[a-helices]]></category>
		<category><![CDATA[a-helix]]></category>
		<category><![CDATA[alhpa helices]]></category>
		<category><![CDATA[alpha helix]]></category>
		<category><![CDATA[b-sheets]]></category>
		<category><![CDATA[b-strand]]></category>
		<category><![CDATA[beta sheets]]></category>
		<category><![CDATA[beta strands]]></category>
		<category><![CDATA[Gor4]]></category>
		<category><![CDATA[HMMSTR]]></category>
		<category><![CDATA[Hnn]]></category>
		<category><![CDATA[JSSPrediction]]></category>
		<category><![CDATA[Jufo]]></category>
		<category><![CDATA[NN-predict]]></category>
		<category><![CDATA[Porter]]></category>
		<category><![CDATA[Prof]]></category>
		<category><![CDATA[PSA]]></category>
		<category><![CDATA[Psipred]]></category>
		<category><![CDATA[Sam]]></category>
		<category><![CDATA[secondary structure]]></category>
		<category><![CDATA[secondary structure prediction]]></category>
		<category><![CDATA[Yaspin]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=456</guid>
		<description><![CDATA[The importance of secondary structure prediction to bioinformatics, modeling and structure prediction cannot be overstated. In a somewhat recent paper by Palopoli et al., their group found that combining the results of mutliple algorithms (with their JSSPrediction methodology) gave major improvements in prediction accuracy (see table at right). This &#8216;combine and conquer&#8217; strategy is a [...]]]></description>
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		<slash:comments>3</slash:comments>
		</item>
		<item>
		<title>What is your favorite journal in the field of computational structural biology?</title>
		<link>http://rosettadesigngroup.com/blog/353/what-is-your-favorite-journal-in-the-field-of-computational-structural-biology/</link>
		<comments>http://rosettadesigngroup.com/blog/353/what-is-your-favorite-journal-in-the-field-of-computational-structural-biology/#comments</comments>
		<pubDate>Thu, 23 Apr 2009 18:56:45 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Polls]]></category>
		<category><![CDATA[Computational Structural Biology]]></category>
		<category><![CDATA[journal]]></category>
		<category><![CDATA[poll]]></category>
		<category><![CDATA[Title Madness]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=353</guid>
		<description><![CDATA[Of course we're all reading all of the journals below, and certainly each has its own benefits. Nontheless, we urge you to pick one and try to explain in the comments what makes that journal special.]]></description>
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		<slash:comments>8</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>
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		<slash:comments>0</slash:comments>
		</item>
		<item>
		<title>What is your favorite molecular viewer ?</title>
		<link>http://rosettadesigngroup.com/blog/284/what-is-your-favorite-molecular-viewer/</link>
		<comments>http://rosettadesigngroup.com/blog/284/what-is-your-favorite-molecular-viewer/#comments</comments>
		<pubDate>Sun, 15 Mar 2009 18:26:52 +0000</pubDate>
		<dc:creator>Nir London</dc:creator>
				<category><![CDATA[Polls]]></category>
		<category><![CDATA[Chimera]]></category>
		<category><![CDATA[Jmol]]></category>
		<category><![CDATA[molecular viewer]]></category>
		<category><![CDATA[PyMOL]]></category>
		<category><![CDATA[Rasmol]]></category>
		<category><![CDATA[Swiss PDB Viewer]]></category>
		<category><![CDATA[visualization]]></category>
		<category><![CDATA[VMD]]></category>

		<guid isPermaLink="false">http://rosettadesigngroup.com/blog/?p=284</guid>
		<description><![CDATA[One of the main tools of the structural biologist (computational or experimental) if not, THE main tool, is the molecular viewer he uses. There are various viewers available, but usually each of us, at a certain point at his career, chooses a specific one and specializes in it. It becomes a way of self expression, to the point that using a "non-native" viewer is like talking in a foreign language. (How do I select only the polar atoms within 4.5A of chain B and color them CPK in this awkward viewer ?!?!?! On MY viewer it would take me a second!) What's your favorite molecular viewer ? help it win this poll!]]></description>
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		<slash:comments>61</slash:comments>
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