Macromolecular Modeling Blog ™

(more…)

In a recent Science paper, Sarel Fleishman et al. report the de-novo computational design of a protein interface to specifically target and tightly bind a surface patch of the flu hemaglutinin protein. We interview Sarel to get the insights from behind the scenes and the outlook for this exciting approach.

(more…)

Three articles recently published in PLoS ONE are the harbinger of a RosettaCon 2010 PLoS one collection. How do you design a new enzyme from scratch? How do you model peptide binding with almost no prior information? And what puzzles CAN’T Rosetta solve?

(more…)

Rosetta 3.2 is the first rosetta release in over a year and is chock-full of new features. Get your (free for academia) copy at: www.rosettacommons.org/software and find the new and improved documentation at: www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide

What’s new in Rosetta 3.2 ?

“Automatic” Comparative Modeling: build structural models of proteins using one or more known structures as templates for modeling.

Flexible Peptide Docking: create high-resolution models of complexes between flexible peptides and globular proteins, starting from approximate, coarse-grain models.

Symmetric Docking: predict the structure of symmetric homooligomeric protein assemblies starting from the structure of a single subunit. The relative subunit orientation and conformations of side-chains are simultaneously optimized for a symmetric protein assembly.

RosettaMatch Application: search through a protein backbone (“scaffold”) to find positions where a binding site for a desired small molecule (or biomolecule, in the more general case) target can be introduced.

Molecular Replacement: solve difficult molecular replacement problems. It will generally be used alongside the molecular replacement software Phaser.

Sequence Tolerance: perform specificity prediction and library design (i.e. for phage display, yeast display, or other selection techniques).

The Rosetta macromolecular modeling suite has a very wide range of applications, and although installing and running Rosetta, becomes increasingly easier over the years, some non-experts would still prefer to run it over a comfortable to use web-server. We have assembled here the list of Rosetta applications for which such a web-server exists. Bookmark for future modeling tasks.

(more…)

We present Rosetta FlexPepDock, a novel tool for refining coarse peptide–protein models that allows significant changes in both peptide backbone and side chains. We obtain high resolution models, often of sub-angstrom backbone quality, over an extensive and general benchmark of 89 peptide–protein interactions.

(more…)

In a recent review published in Biochemistry, Kaufmann, Lemmon and DeLuca et al. from the Meiler Lab, cover the Rosetta modeling suite capabilities. More importantly, as supplementary information they provide tutorials to demonstrate 6 basic use cases of Rosetta.

(more…)

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.

(more…)

As in previous years, we would like to invite representatives of the pharma and biotech industry to participate in RosettaCon 2010. Take part in the workshops, seminars, and have an opportunity to meet the Rosetta Commons researchers. Get to know Rosetta from the inside. RosettaCon will take place during August 3-6 at the beautiful Sleeping Lady Mountain Retreat in Leavenworth, Washington, about 2.5 hours outside Seattle, in a dramatic mountain scenery – the only fitting environment for a scientific discussion really.

(more…)

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:

http://www.lulu.com/content/paperback-book/the-pyrosetta-interactive-platform-for-protein-structure-prediciton-and-design-a-set-of-educational-modules/7187010

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