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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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.

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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.

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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.

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Are wikis the future of scientific collaboration in biology? 

The tremendous success of Wikipedia has raised the possibility of using wiki technology for scientific collaboration. However, it is not yet clear if traditional scientific methods can be acceptably incorporated into the ‘wiki’ paradigm. Despite this uncertainty, many tens of ‘scientific-wikis’ currently exist [1], with many more ‘annotation-wikis’ on the horizon. In this post we will discuss two key scientific concepts, and try to assess how they fit (or not) within the ‘wiki’ model. By Dan Bolser and Jong Bhak  (more…)

NCBI’s PubMed has recently added a useful feature for those working with protein structures. When featuring a specific abstract, besides the more familliar “Related articles” you can now find a “Structures reported by this article” pane, with a small illustration, PDB code and even the structure’s resolution.

Anyone who found himself scanning a paper for a desired PDB id, must feel a warm sensation in the chest towards this feature. Perfection is in the details, way to go pubmed.

Pubmed's Reported Structures Feature

It is well known that proteins that share high sequence identity usually share the same fold and approximately the same structure, this is the basis for homology modeling. It also well known that some folds contains proteins with very different sequences. These cases pose a problem for sequence based structural alignments and for sequence based search protocols. For that reason, algorithms were devised to quickly and efficiently search (let’s say – the entire PDB) for proteins with a similar structure although not necessarily with similar sequence. 

We present a list of 5 such algorithms, implemented into a publicly available web-server, for your convenience (some are even available for download). These software relay on sophisticated superposition algorithms and hence you can use most of them to just accurately superimpose two structures. 

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The Outcome of a workshop on applications of protein models in biomedical research. review summarizes a recent meeting (meeting website) held at UCSF. The case studies in this review may serve as an excellent resource for researchers that need to demonstrate the applicability and utility of macromolecular modeling for advancing experimental studies. In the author list from the Rosetta Commons were Tanja Kortemme and Rhiju Das. The author list is also a great resource for those that are new to the field and would like to familiarize themselves with some of the major figures.
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