Macromolecular modeling n00bz, get up to speed with this review

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?



PyRosetta Book

PyRosetta Book

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, refinement, docking and design. The focus is on enabling users to write custom scripts, so it includes material on Rosetta fundamentals and the appendices have a list of PyRosetta commands and a breakdown of the input files. The book was beta-tested by students during a course at JHU. The course is a series of workshops that teach how to measure and manipulate protein conformations, calculate energies in low- and high-resolution representations, fold proteins from sequence, model variable regions of proteins (loops), dock proteins or small molecules, design protein sequences, and build custom protocols for operations tailored to particular biomolecular applications

The book can be purchased through Lulu:


or downloaded for free as pdf chapters from http://www.pyrosetta.org under the Tutorial link.


Macromolecular Modeling for Molecular Systems Engineering

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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