Macromolecular Modeling Blog ™

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 and start to aggregate into fibrils. http://bit.ly/taQ0E3
• Computational Structural Bioinformatics Workshop 2011 Nov 12 8:30-5:00 Atlanta, GA http://www.cs.odu.edu/~lchen/CSBW.htm
• A Protocol for Computer-Based Protein Structure and Function Prediction: http://bit.ly/tgqvXV #in
• Cool blog – The Protein Engineer http://proteneer.com/blog/
• Mapping intact protein isoforms in discovery mode using top-down proteomics http://bit.ly/sC0bBf #citeulike
• Molecular Modeling Software - @biosoftcn avidly tweets and curates bioinformatics and modeling software (collected a…http://ow.ly/1ftAeF
• New blog post: The paper about BioStar has been published in “PLoS Computational Biology”: http://bit.ly/rvOOFV
• Nice post on GPCR modeling and virtual screeninghttp://bit.ly/syitwf
• Best ab-initio structure prediction tool? http://bit.ly/rW4R2q Come on BioStar, you can do better than this… #BioStar
• RT @CellCellPress: A Protein Complex Network of Drosophila melanogaster: http://bit.ly/vsJdqg #bioinformatics
• Olympic Crystal Packing – In the spirit of the 2012 Olympic games. Found at the webpage of the group of Prof. Heinz …http://ow.ly/1fttni
• Seminar: Computational Design of Protein Interfaces and Switches – Brian Kuhlman. EB1 1011, Nov 7, 10:40AM http://dld.bz/axf4R

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.

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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?

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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. So here is a pilot for this approach, let’s see how it goes. All the titles are posted as comments at the bottom, you can comment/ask questions on specific ones, show appreciation by ‘liking’ them, sort by popularity, moreover – you can add all the ones I missed!

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, as well as recently, a completely unrelated theoretical evolutionary paper just to broaden our horizons.

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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.

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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.

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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.
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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.

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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.

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