Macromolecular Modeling Blog ™

Another compilation of forty some titles from the recent literature all about your favorite computational structural biology science. Two of the papers are by Rosetta Design Group’s members – see if you can find waldo. Enjoy.

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This is the fifth and last post in the CAPRI series, summarizing the presentations of Xiaoqin Zou and Ora Schueler-Furman (Saving the best for last..), as provided by the speakers. I hope the CAPRI series was able to give a snapshot of the state of computational protein-protein docking and its community. I want to thank again to everyone that took part in the meeting and helped me with this series.

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Traditionally, computational protein design efforts have been directed at calculating a single sequence predicted to fold to a particular target structure. Recently, however, a number of conceptual generalizations have been pursued, ranging from the use of backbone flexibility, off-rotamer side chain flexibility, negative design, multi-body potentials, conformational free energy, and prediction of sequence profiles. Below I present our state-of-the-art research whose goal is to understand how protein sequences are optimized to be compatible with binding multiple partners with high affinity. – By Menachem Fromer.

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This is the fourth post in the CAPRI series, summarizing the presentations of Paul Bates, Martin Zacharias, and Carlos Camacho, as provided by the speakers. More to appear in the continuation of the series.

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You know the drill… a collection of relevant titles from the recent literature, if you want to discuss any of these, or expand on them, we’ll be more than happy.

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This is the third post in the CAPRI series, summarizing the presentations of Jeffrey Gray, Zhiping Weng, and Miriam Eisenstein, as provided by the speakers. More to appear in the continuation of the series.
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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.

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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?

A beautiful post by Michael Clarkson on a beautiful work by himself and friends, published in Nature. It’s always nice when a fellow blogger gets to present his own work. Post is re-blogged as is from “Discount Thoughts”.

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