Macromolecular Modeling Blog ™

Over the past decade it has become evident that many proteins have disordered regions, even in their native states. Moreover, entire proteins were found to be intrinsically disordered. These have several names, such as disordered proteins, unstructured proteins, intrinsically unfolded proteins, and others, as well as several functions, but perhaps the most studied function is their binding to different proteins in the cell.

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Another year went by, and there is still modeling work to be done. 2009 was a good year for the “Macromolecular Modeling Blog”. The number of subscribers almost quadrupled. We have several hundreds of twitter followers, and a twitter modelers list. And best of all we are still enjoying what we do.

What will happen in the blog in 2010?

* We’re working on a project covering the “state of the nation” in protein-protein docking, following the 4th CAPRI evaluation meeting, that should be posted as a series in the beginning of the year.
* Following good feedback on the “Molecular Modeling Jobs” post, we’re working on establishing (and updating) a Jobs section.
* Some new people will start writing for the Blog (Do YOU want to post at the Macromolecular Modeling Blog? contact us)
* You’ll read more reviews and literary digests.
* All that is interesting for modelers – what would you want to see here in 2010? tell us in the comments.

Good modeling “Karma”

It is a well known fact amongst modelers that the “true” energy function contains an extra energy term (which is by no means a two-body term) called the modeling “Karma”. Do you want to have good modeling Karma in 2010?

* Share this post with 5 friends and a structure will be published instead of that homology model you were working with.
* Share this post with 10 friends and your models will display sub-angstrom accuracy.
* Share this post with 15 friends and an experimental collaborator will call in with some good news.
* Share this post with 20 friends or more and we assure you that you’ll lend that R01 NIH grant in 2010.

Good Modeling Karma

We wish all our readers a very happy New Year and the best modeling Karma

Last month in Nature Chemical Biology, Dan Mandell and Tanja Kortemme from UCSF published a great review of current research in macromolecular modeling and experimentation: Computer-aided design of functional protein interactions. The review focuses on protein-protein interactions and interfaces but also covers the general field of macromolecular modeling in some depth. It includes sections that introduce basic concepts in modeling and tables that provide a succinct snapshot of recent accomplishments and how they tie in to the greater field.

Having finished reviewing a review, I will be following Borges’ lead and review papers from the literature that have not yet been written. Any paper suggestions?

The NIH recently announced a proposal solicitation for use of the Blue Waters petascale computing system.

They will be giving a videocast on December 17th and of course molecular modeling is at the top of the list of priorities:

“Because of the considerable NIGMS investment in protein folding and prediction of protein structure from sequence, we will explore this area during the videocast.”

See the full post on the NIGMS Feedback Loop Blog.

A beautiful post by Michael Clarkson on a beautiful work by himself and friends, published in Nature. It’s always nice when a fellow blogger gets to present his own work. Post is re-blogged as is from “Discount Thoughts”.

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50 papers of potential interest from the (very) recent literature.

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