Macromolecular Modeling Blog ™

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This is the first post in a series, summarizing the CAPRI (Critical Assessment of PRediction of Interactions) 4th Evaluation meeting. In this post I’ll try to give a more personal perspective of the experiment results, the state and trends of computational protein-protein docking and the vibes behind the scenes. The next posts in the series will shortly summarize select talks from the meeting, kindly provided by the speakers.

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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

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 as some other interesting protein engineering. This is a conference aimed significantly at industry, but should be interesting to academics looking for connections between their work and the world of biotech/pharma.

More Info: Website / Brochure

By Jonathan Davis.

Jonathan Davis is a Principal Scientist in Protein Design at Adnexus, a Bristol-Myers Squibb R&D Company.

RosettaCon 2009 has ended just a few days ago.

This was a very exciting meeting, gathering almost all Rosetta developers from around the world, and representatives of the major industry licensees of Rosetta. The talks were quite diverse, ranging from new Rosetta protocols under development, applications with regards to numerous biological systems, and up to code architecture and future development of the code.

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. A modeler’s utopia.
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Next week, RDG will be teaching a three day course at the Center of Information Technology of the National Institutes of Health:

#468 Rosetta Hands-On Workshop

Please see the RosettaDock Webinar post for more details.

The Annual International Meeting of the Molecular Graphics and Modeling Society (MGMS) will take place in Erlangen, Germany from September 7th (registration and mixer) – 11th 2009.

The meeting will be preceded by the annual Molecular Modelling Workshop organised by the Molecular Graphics and Modelling Society – Deutschsprachige Sektion (MGMS-DS) from Sunday 6th to Monday, September 7th.

More Details: Modeling’09

The RCSB PDB will host a short course for practicing modelers looking for a better understanding of crystal structures and PDB data.

Dates: May 7 & 8 at Rutgers, The State University of New Jersey in Piscataway, NJ.

The target audience is PDB data users working in pharmaceuticals, biologicals, chemical industries, academia, and others who are looking to understand how to interpret in crystal structure data: possible problems, errors, and accuracy; how the data is determined and annotated; and what information and data is provided beyond atomic coordinates.

To learn more and register: Crystallography for Modelers

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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