Andrew Leaver-Fay

发表

Specific tests for Rosetta running on our automated testing framework.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

An Adaptive Dynamic Programming Algorithm for the Side Chain Placement Problem

Jack Snoeyink, Andrew Leaver-Fay, Brian Kuhlman, 2004, Pacific Symposium on Biocomputing.

Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design

Andrew Watkins, Krishna Praneeth Kilambi, P. Douglas Renfrew, 2013, PloS one.

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design.

Brian D. Weitzner, Roland L. Dunbrack, Sergey Lyskov, 2020, Biophysicist.

Predicting protein structures with a multiplayer online game

Adrien Treuille, Andrew Leaver-Fay, David Baker, 2010, Nature.

Typical development workflow in the Rosetta community.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Capturing atomic interactions with a graphical framework in computational protein design

Jack Snoeyink, Andrew Leaver-Fay, J. Snoeyink, 2006 .

Values Statement: Equality and Inclusion in the RosettaCommons.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Better together: Elements of successful scientific software development in a distributed collaborative community

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020, PLoS Comput. Biol..

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.

Jens Meiler, Florian Richter, David Baker, 2011, Methods in enzymology.

Growth in Rosetta PIs and conference attendees.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Modeling Symmetric Macromolecular Structures in Rosetta3

David Baker, Andrew Leaver-Fay, Frank DiMaio, 2011, PloS one.

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Brian D. Weitzner, Lars Malmström, Karen R. Khar, 2020, Nature Methods.

Details of Remaining Collective Challenges.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Resource Computationally Designed Bispecific Antibodies using Negative State Repertoires Graphical Abstract Highlights

Andrew Leaver-Fay, Brian Kuhlman, Karen J. Froning, 2016 .

Maintaining solvent accessible surface area under rotamer substitution for protein design

Jack Snoeyink, Andrew Leaver-Fay, Brian Kuhlman, 2007, J. Comput. Chem..

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta

David Baker, Andrew Leaver-Fay, Seth Cooper, 2017, Bioinform..

Faster placement of hydrogens in protein structures by dynamic programming

Jack Snoeyink, Andrew Leaver-Fay, Yuanxin Liu, 2008, JEAL.

Commercial spin-off companies from the Rosetta community.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

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

Jens Meiler, Florian Richter, Sarel J. Fleishman, 2011, PloS one.

A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design

Andrew Leaver-Fay, Jeffrey J. Gray, Jeffrey J. Gray, 2017, PLoS Comput. Biol..

The challenge of designing scientific discovery games

David Salesin, Adrien Treuille, Andrew Leaver-Fay, 2010, FDG.

The Rosetta all-atom energy function for macromolecular modeling and design

Roland L. Dunbrack, Richard Bonneau, P. Douglas Renfrew, 2017, bioRxiv.

On-the-Fly Rotamer Pair Energy Evaluation in Protein Design

Jack Snoeyink, Andrew Leaver-Fay, Brian Kuhlman, 2008, ISBRA.

Rotamer-Pair Energy Calculations Using a Trie Data Structure

Jack Snoeyink, Andrew Leaver-Fay, Brian Kuhlman, 2005, WABI.

Nucleic Acids Research Advance Access published April 22, 2007 MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

Jack Snoeyink, Andrew Leaver-Fay, Xueyi Wang, 2007 .

Descriptions of the Rosetta board positions.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

Scientific benchmarks for guiding macromolecular energy function improvement.

Jack Snoeyink, Yifan Song, James Thompson, 2013, Methods in enzymology.

Members of the RosettaCommons Consortium.

Brian D. Weitzner, Jens Meiler, Roland L. Dunbrack, 2020 .

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design

Brian D. Weitzner, Roland L. Dunbrack, Sergey Lyskov, 2021 .

A Generic Program for Multistate Protein Design

Andrew Leaver-Fay, Brian Kuhlman, Ron Jacak, 2011, PloS one.

De Novo Enzyme Design Using Rosetta3

David Baker, Andrew Leaver-Fay, Sagar D. Khare, 2011, PloS one.

Computational design of a PAK1 binding protein.

Thomas Szyperski, Andrew Leaver-Fay, Brian Kuhlman, 2010, Journal of molecular biology.

Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface

Andrew Leaver-Fay, Brian Kuhlman, Steven M Lewis, 2014, Nature Biotechnology.