Advertisement

Table of Contents: RosettaCon 2012

COVER

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

The Rosetta macromolecular modeling, prediction, and design software suite is supported by a large developer community and enjoys a diverse user base. Each year Rosetta developers and users from academia and industry meet to discuss improvements and new code, as well as exciting, emerging applications.

This Collection draws from material presented at RosettaCon 2012. The Collection is meant to both highlight new scientific developments within the Rosetta community and provide a rigorously reproducible workflow for each protocol. This year's Collection highlights exciting advances that increase the usability of Rosetta, improve current methods, and introduce completely new protocols.

Collection Citation: RosettaCon 2012 (2013)

PLOS Collections: http://www.ploscollections.org/rosettacon2012

Overview

Research Articles

Cross-Link Guided Molecular Modeling with ROSETTA

Abdullah Kahraman, Franz Herzog, Alexander Leitner, George Rosenberger, Ruedi Aebersold, Lars Malmström

RosettaEPR: Rotamer Library for Spin Label Structure and Dynamics

Nathan S. Alexander, Richard A. Stein, Hanane A. Koteiche, Kristian W. Kaufmann, Hassane S. Mchaourab, Jens Meiler

Fast Docking on Graphics Processing Units via Ray-Casting

Karen R. Khar, Lukasz Goldschmidt, John Karanicolas

Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design

Kevin Drew, P. Douglas Renfrew, Timothy W. Craven, Glenn L. Butterfoss, Fang-Chieh Chou, Sergey Lyskov, Brooke N. Bullock, Andrew Watkins, Jason W. Labonte, Michael Pacella, Krishna Praneeth Kilambi, Andrew Leaver-Fay, Brian Kuhlman, Jeffrey J. Gray, Philip Bradley, Kent Kirshenbaum, Paramjit S. Arora, Rhiju Das, Richard Bonneau

Assessment and Challenges of Ligand Docking into Comparative Models of G-Protein Coupled Receptors

Elizabeth Dong Nguyen, Christoffer Norn, Thomas M. Frimurer, Jens Meiler

Alternative Computational Protocols for Supercharging Protein Surfaces for Reversible Unfolding and Retention of Stability

Bryan S. Der, Christien Kluwe, Aleksandr E. Miklos, Ron Jacak, Sergey Lyskov, Jeffrey J. Gray, George Georgiou, Andrew D. Ellington, Brian Kuhlman

Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)

Sergey Lyskov, Fang-Chieh Chou, Shane Ó. Conchúir, Bryan S. Der, Kevin Drew, Daisuke Kuroda, Jianqing Xu, Brian D. Weitzner, P. Douglas Renfrew, Parin Sripakdeevong, Benjamin Borgo, James J. Havranek, Brian Kuhlman, Tanja Kortemme, Richard Bonneau, Jeffrey J. Gray, Rhiju Das

A Pareto-Optimal Refinement Method for Protein Design Scaffolds

Lucas Gregorio Nivón, Rocco Moretti, David Baker