Macromolecular Modeling Blog ™

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

Following the success of our previous poll which was followed by an extensive and interesting discussion, and in order to better our Bi(Tri,..)-Weekly Digests, we present a new poll which will determine once and for all, which is the best journal for the computational structural biologist. 

Of course we’re all reading all of the journals below, and certainly each has its own benefits. There is also the question if by “favorite” journal we mean where would you like to publish, or which are you enjoying reading the most? We know the question isn’t adequately defined. Nontheless, we urge you to pick one and try to explain in the comments what makes that journal special.

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Update: additional journals proposed by the readers (which fall under the “other” category): JMB, Biochemistry, Protein science, Protein engineering, Journal of Medicinal Chemistry, Journal of Computer-Aided Molecular Design, Journal of Molecular Modeling, Journal of Chemical Information and Modeling, BMC Structural Biology, Biopolymers & BMC Bioinformatics. Keep ‘em coming.

Did we miss the best Journal of them all? Tell us in the comments and we’ll add it to the poll.

Macromolecular systems engineering can help us meet some of the most important technological challenges in the world today, ranging from medicine to renewable energy, and the development of better-integrated computational design tools will accelerate progress. Macromolecular modeling capabilities are advancing rapidly, but much of their potential for supporting systems engineering has yet to be exploited. In this post, I’d like to describe the fundamental nature of the problems and outline some of what needs to be done to make their potential a reality. By Dr. Eric Drexler.

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In a recent Nature paper Koder & Anderson et al. describe the procedure for creating an O2 transport protein from first principals. The paper is somewhat technical and may appeal to the biochemists amongst our readers, here we present the main ideas, findings and conclusions. 

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