Macromolecular Modeling Blog ™

PyRosetta

Xavier Ambroggio — Mon, 09 Nov 2009 17:56:55 +0000

The Gray Lab at Johns Hopkins University has just released PyRosetta, a Python-based interactive platform for accessing the objects and algorithms within the Rosetta protein structure prediction suite. In addition to the code, the Gray Lab has put together a book that leads the reader through basics of protein structure and energetics to applications in folding, [...]

Modeling literature digest - it’s back..

Nir London — Sat, 07 Nov 2009 16:58:53 +0000

After a long break, the molecular modeling literature digest is back with ~50 recent publication which we believe would be of interest. As usual you are most welcome to add relevant publications or suggest specific papers for us to focus on.

Warren DeLano has passed away, a terrible tragedy.

Xavier Ambroggio — Fri, 06 Nov 2009 03:22:11 +0000

We recently saw these posts reporting that Warren DeLano passed away on Tuesday: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;19EK9w;20091105105413-0800 http://www.macresearch.org/memoriam-warren-l-delano This is a terrible tragedy and our hearts go out to his family and friends. He was a truly incredible person whose work with PyMOL changed the face of molecular modeling. He also had a huge personal impact on our community. He was [...]

Which is the fairest secondary structure prediction algorithm of them all?

Xavier Ambroggio — Fri, 30 Oct 2009 21:26:15 +0000

The importance of secondary structure prediction to bioinformatics, modeling and structure prediction cannot be overstated. In a somewhat recent paper by Palopoli et al., their group found that combining the results of mutliple algorithms (with their JSSPrediction methodology) gave major improvements in prediction accuracy (see table at right). This ‘combine and conquer’ strategy is a [...]

Dynamic interactions of proteins in complex networks: a more structured view.

Nir London — Wed, 28 Oct 2009 17:55:19 +0000

This recent mini-review by Stein et al. focuses on the mechanisms that enable dynamic, transient, short lived interactions in cellular networks. Of special interest are the always popular "motif recognition domain"-"short flexible peptide" interactions. However, post translational modifications and regulation by disorder are also discussed. We concise the review further to some basic/interesting/anecdotal/"pondering worthy" points.

Interactive 3D Molecules in articles

Nir London — Sat, 24 Oct 2009 08:29:47 +0000

PLoS ONE launched a new collection titled “Structural Biology and Human Health: Medically Relevant Proteins from the SGC” which makes use of three dimensional molecular animation technology.

We’ve got Aspergers.

Xavier Ambroggio — Thu, 24 Sep 2009 03:15:20 +0000

My jaw dropped when I saw this. Hilarious. Scary. So true. Its from: http://en.wikipedia.org/wiki/Asperger_syndrome

LinkedIn groups related to macromolecular modeling

Xavier Ambroggio — Thu, 10 Sep 2009 15:18:49 +0000

A variety of groups have sprung up on LinkedIn that may be of interest to macromolecular modelers. In these groups, there are job postings, literature reviews and notices, discussions, and more. Below is a list of groups that we have joined. Do you know of a group that is not listed below? Antibody Network Biotech & [...]

IBC’s 4th Annual Beyond Antibodies / Protein Engineering & Design Conference

admin — Fri, 21 Aug 2009 15:30:58 +0000

When: September 21-23, 2009 Where: Town and Country Hotel, San Diego, CA What: I’m writing to let you know about a conference taking place next month in San Diego, that has a new parallel conference called “Protein Engineering and Design”. I’m chairing the last day’s sessions, and there are a few Rosetta-based talks in them as well [...]

RosettaCon 2009 - perspective

Nir London — Mon, 10 Aug 2009 23:01:15 +0000

... For scientists specializing in a specific field (such as computational structural biology - just off the top of my head) there are rare occasions in which meetings are dedicated entirely to their topic. This was such a conference! All through the three days of conference and one day of hiking, people had talked, discussed, brain stormed, ate, breathed, thought, swam, hiked, mingled and laughed protein structure. If the coffee break was drawn as a comic figure, with bubble clouds to depict thoughts and conversations, it would be a sea of alpha-helices, weird looking loops, rotamers, ligands and co-factors at interfaces, strange folds and stranger rainbow colored cartoon proteins...