Macromolecular Modeling Blog ™

We launched a new Jobs page.

If you’re looking to hire – fill in the form at the top of the page. If you’re looking for a molecular modeling job – search the jobs (posted in reverse chronological date)

Molecular Modeling Jobs

We hope this resource would help both employers and modelers.

Are you tired of manually editing PDB files ?

Checkout this PDB mode for Emacs that helps you do most of the usual modeler editing tasks in a press of a button.

Via @leninwtigger

In a recent review published in Biochemistry, Kaufmann, Lemmon and DeLuca et al. from the Meiler Lab, cover the Rosetta modeling suite capabilities. More importantly, as supplementary information they provide tutorials to demonstrate 6 basic use cases of Rosetta.

(more…)

NAR just published the new special “Database” issue for 2010. We collected 23 papers that might be of interest to structural biologists, modelers and other protein people.

(more…)

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.

(more…)

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.

As from next week, the RCSB PDB will provide web widgets – small bits of code, which provide PDB functionality that you can embed in your own website. All of the widgets that are provided are 100% self contained JavaScript files and will be maintained by the RSCB PDB. We’ve taken some of those widgets for a test drive.

(more…)

Several positions for molecular modelers have recently came to our attention. We thought some of our readers might express interest in these opportunities. If you find this type of service helpfull/annoying please let us know in the comments. If you wish to post available positions in the molecular modeling field please contact us.

(more…)

Roland Dunbrack shows off the capabilities of SCWRL4, the new version of his famous side chain prediction software. Indeed it seems that the new version has come a long way, especially in the form of a new, smoother backbone-dependent rotamer library. Roland promises to answer any questions regarding the new rotamer library, SCWRL, and also random questions.

(more…)