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Table of Contents: RosettaCon 2010

COVER

Image Credit: Chris Poultney, Richard Bonneau, New York University
Issue Image

The Rosetta framework for macromolecular modeling, prediction and design is a widely used code (over 7,000 registered groups) with a large, dynamic developer community (over 200 members). The Rosetta community, which includes developers and users from industry and academia, meets once a year to discuss improvements to Rosetta, new applications of the Rosetta code to biological and chemical problems, and core code development. This special collection (PLoS One Special collection: RosettaCon 2010) presents recent developments from the Rosetta community, drawn from the groups participating in RosettaCon 2010.

The collection focuses on the publication of both the science and the reproducible computational workflow: each paper is accompanied by an annotated archive containing the code, scripts and data-sets needed to carry out the computational protocol described in the paper.

Articles are presented in order of publication date and new articles will be added to the Collection as they are published.

Editorial oversight, and coordination of the peer-review, was provided by Vladimir Uversky, PLoS ONE Academic Editor.

Collection Citation: RosettaCon 2010 (2011) PLoS Collections: http://www.ploscollections.org/RosettaCon2010

Overview

The 2010 Rosetta Developers Meeting: Macromolecular Prediction and Design Meets Reproducible Publishing

P. Douglas Renfrew, Gabrielle Campbell, Charlie E. M. Strauss, Richard Bonneau

Research Articles

Rational Design of Temperature-Sensitive Alleles Using Computational Structure Prediction

Christopher S. Poultney, Glenn L. Butterfoss, Michelle R. Gutwein, Kevin Drew, David Gresham, Kristin C. Gunsalus, Dennis E. Shasha, Richard Bonneau

RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design

Po-Ssu Huang, Yih-En Andrew Ban, Florian Richter, Ingemar Andre, Robert Vernon, William R. Schief, David Baker

Generalized Fragment Picking in Rosetta: Design, Protocols and Applications

Dominik Gront, Daniel W. Kulp, Robert M. Vernon, Charlie E. M. Strauss, David Baker

Real-Time PyMOL Visualization for Rosetta and PyRosetta

Evan H. Baugh, Sergey Lyskov, Brian D. Weitzner, Jeffrey J. Gray

Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2

Sidhartha Chaudhury, Monica Berrondo, Brian D. Weitzner, Pravin Muthu, Hannah Bergman, Jeffrey J. Gray

Modeling Disordered Regions in Proteins Using Rosetta

Ray Yu-Ruei Wang, Yan Han, Kristina Krassovsky, William Sheffler, Michael Tyka, David Baker

A Generic Program for Multistate Protein Design

Andrew Leaver-Fay, Ron Jacak, P. Benjamin Stranges, Brian Kuhlman

RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite

Sarel J. Fleishman, Andrew Leaver-Fay, Jacob E. Corn, Eva-Maria Strauch, Sagar D. Khare, Nobuyasu Koga, Justin Ashworth, Paul Murphy, Florian Richter, Gordon Lemmon, Jens Meiler, David Baker

Modeling Symmetric Macromolecular Structures in Rosetta3

Frank DiMaio, Andrew Leaver-Fay, Phil Bradley, David Baker, Ingemar André

Anchored Design of Protein-Protein Interfaces

Steven M. Lewis, Brian A. Kuhlman

De Novo Enzyme Design Using Rosetta3

Florian Richter, Andrew Leaver-Fay, Sagar D. Khare, Sinisa Bjelic, David Baker