Biology & Life Sciences

RosettaCon 2012

Published June 8, 2016 Partnered Collections

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. It 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.

Image Credit: journal.pone.0023947

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Overview
From the Blogs
Research Articles

Overview

Image credit
Chris Poultney, Richard Bonneau, New York University

PLOS ONE The RosettaCon 2012 Special Collection: Code Writ on Water, Documentation Writ in Stone
September 26, 2013 Ingemar André, Jacob Corn

From the Blogs

Image credit
Chris Poultney, Richard Bonneau, New York University / PLOS

EveryONE The RosettaCon 2012 Collection: Rosetta Developers Meet the Challenges in Macromodeling Head On
September 26, 2013 Jen Laloup

Research Articles

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10.1371/journal.pone.0073411

PLOS ONE Cross-Link Guided Molecular Modeling with ROSETTA
September 17, 2013 Abdullah Kahraman, Franz Herzog, Alexander Leitner, George Rosenberger, Ruedi Aebersold, Lars Malmström
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10.1371/journal.pone.0072851

PLOS ONE RosettaEPR: Rotamer Library for Spin Label Structure and Dynamics
September 5, 2013 Nathan Alexander, Richard Stein, Hanane Koteiche, Kristian Kaufmann, Hassane Mchaourab, Jens Meiler
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10.1371/journal.pone.0072096

PLOS ONE Replica Exchange Improves Sampling in Low-Resolution Docking Stage of RosettaDock
August 29, 2013 Zhe Zhang, Oliver Lange
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10.1371/journal.pone.0070661

PLOS ONE Fast Docking on Graphics Processing Units via Ray-Casting
August 16, 2013 Karen Khar, Lukasz Goldschmidt, John Karanicolas
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10.1371/journal.pone.0067051

PLOS ONE Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design
July 15, 2013 Kevin Drew, P. Douglas Renfrew, Timothy Craven, Glenn Butterfoss, Fang-Chieh Chou, Sergey Lyskov, Brooke Bullock, Andrew Watkins, Jason Labonte, Michael Pacella, Krishna Kilambi, Andrew Leaver-Fay, Brian Kuhlman, Jeffrey Gray, Philip Bradley, Kent Kirshenbaum, Paramjit Arora, Rhiju Das, Richard Bonneau
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10.1371/journal.pone.0066856

PLOS ONE The PyRosetta Toolkit: A Graphical User Interface for the Rosetta Software Suite
July 9, 2013 Jared Adolf-Bryfogle, Roland Dunbrack
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10.1371/journal.pone.0067302

PLOS ONE Assessment and Challenges of Ligand Docking into Comparative Models of G-Protein Coupled Receptors
July 2, 2013 Elizabeth Nguyen, Christoffer Norn, Thomas Frimurer, Jens Meiler
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10.1371/journal.pone.0067536

PLOS ONE Towards Ligand Docking Including Explicit Interface Water Molecules
June 28, 2013 Gordon Lemmon, Jens Meiler
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10.1371/journal.pone.0064363

PLOS ONE Alternative Computational Protocols for Supercharging Protein Surfaces for Reversible Unfolding and Retention of Stability
May 31, 2013 Bryan Der, Christien Kluwe, Aleksandr Miklos, Ron Jacak, Sergey Lyskov, Jeffrey Gray, George Georgiou, Andrew Ellington, Brian Kuhlman
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10.1371/journal.pone.0063906

PLOS ONE Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)
May 22, 2013 Sergey Lyskov, Fang-Chieh Chou, Shane Conchúir, Bryan Der, Kevin Drew, Daisuke Kuroda, Jianqing Xu, Brian Weitzner, P. Renfrew, Parin Sripakdeevong, Benjamin Borgo, James Havranek, Brian Kuhlman, Tanja Kortemme, Richard Bonneau, Jeffrey Gray, Rhiju Das
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10.1371/journal.pone.0063090

PLOS ONE Improvements to Robotics-Inspired Conformational Sampling in Rosetta
May 21, 2013 Amelie Stein, Tanja Kortemme
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10.1371/journal.pone.0059004

PLOS ONE A Pareto-Optimal Refinement Method for Protein Design Scaffolds
April 2, 2013 Lucas Nivón, Rocco Moretti, David Baker