Macromolecular Modeling Blog ™

Check out the Jobs Board for a new opening from Intrexon and others: http://rosettadesigngroup.com/blog/molecular-modeling-jobs/

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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 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?

Olympic Crystal Packing

HT to ravehb for the finding.

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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We are excited to announce our Stanford-Sweden summer modeling workshop, to be held in Uppsala 20-22 June. This workshop brings together scientists from the Bay Area, Sweden, and the wider world to discuss late-breaking research on simulation of macromolecules and complexes, spanning levels of resolution from coarse to fine. We will discuss structure prediction, dynamics, sampling, assembly, and aggregation from both a computational and experimental perspective. We will also give tutorials on simulation software, such as SimTK Simbody, DOCK_Blaster, and MMB/RNABuilder. Please post the attached flyer on your departmental email list, on physical bulletin boards, or otherwise circulate widely. Details on the program will be posted on our event page as they become available: http://xray.bmc.uu.se/flores/Stanford-Sweden-workshop-2011

Thanks, and hope you can make it!

Samuel Flores, Johan Åqvist, Erik Lindahl, and Michael Levitt

About the author: Samuel Flores (samuelfloresc AT gmail.com): I write easy to use multiresolution modeling software which helps predict how large biological molecules form and move. I and my collaborators have applied it to lots of problems, such as group I and group II intron structure, ribosome hybridization, and telomerase elongation. I’m also working on antibody design and other viral applications. Currently I’m extending my software, MMB, to handle huge complexes even more efficiently. A new feature called “physics where you want it” will let you apply a physics-based force field to a restricted region of your complex, e.g. an active site or interface, while treating the rest with coarser forces and kinematics. MMB will also start reading electron densities and other experimental data, expanding the types of constraints that can be used for modeling.