Macromolecular Modeling Blog ™

Incorporation of flexibility into docking simulations and accounting for backbone conformational changes during association is probably the toughest problem protein-protein dockers are facing today. Normal Mode Analysis is lately the answer of many groups to this problem. We hereby review two approaches of incorporating NMA into docking simulations, reflecting the induced fit vs. conformational sampling association mechanisms. 

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In this weekly digest – relevant titles form current issues of Nature Structural and Molecular Biology, Bioinformatics, BMC Bioinformatics, Plos Computational Biology and Journal of Computational Biology. If you want to initiate in a public discussion on one of these, let us know in the comments.

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Checkout these decent looking, ad-free, macromolecular modeling wallpapers from the San Diego Supercomputer Center’s Multimedia Gallery:

Predicting Protein Structures (our favorite!!)
Understanding Parkinson’s Disease
A Novel Twist on Virus DNA
Fighting Bird Flu
Unraveling the Secrets of Spider Silk
Fighting Bird Flu (2)
Targeting African Sleeping Sickness
Virus in Three Dimensions (2nd favorite, 1st if I was being objective)
Visualizing a Viral Protein Coat
Learning about Lipids
Accurately Predicting Protein Docking

Here is a modified version of my second favorite for Macs:

In this version the virus looks either like the sun or an invading alien depending on your disposition.

Enjoy!

In a paper published by PLOS Computational Biology, Sonavane et al. presents an analysis of cavities within the structures of protein monomers, as well as for protein-protein interfaces. We present their main findings. By Nir London

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Dear readership,

The Macromolecular Modeling Blog is up and running for a month now. We have received good feedback and visitor influx speaks volumes, so I know there is at least someone (several ? ) out there reading these lines… At this point we would like to consult with you on the content and format YOU want to read.

One of the services we provided is a continues literature screening, from which, papers of interest were reported in the “Title Madness” posts. Part of the underlying rational was that we wanted to engage in a discourse about specific papers. We decided to move this activity to a “Title Madness” page that would be updated regularly, partly because we were running out of roman numerals, partly because an endless stream of titles posts might be annoying. What do you prefer ? weekly digests ? specific abstracts ? 

What other content related to macromolecular modeling would you want to see in our blog ? go wild, any ideas will be welcomed.. share with us in the comments and a happy first month anniversary to us all.

By Nir London