Andrew Leaver-Fay

发表

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

Vincent B. Chen, Ian W. Davis, Jeremy N. Block, 2007, Nucleic Acids Res..

Macromolecular modeling and design in Rosetta: recent methods and frameworks

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

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.

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design.

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

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

Roland L. Dunbrack, Jason W. Labonte, Jeffrey J. Gray, 2017, bioRxiv.

Scientific benchmarks for guiding macromolecular energy function improvement.

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

Modeling Symmetric Macromolecular Structures in Rosetta3

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

Structure-guided forcefield optimization

D. Baker, James M Thompson, M. Tyka, 2011, Proteins.

Computational design of a PAK1 binding protein.

Shuangye Yin, B. Kuhlman, N. Dokholyan, 2010, Journal of molecular biology.

Computational design of a PAK1 binding protein.

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

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

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

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

Vincent B. Chen, Ian W. Davis, Jeremy N. Block, 2007 .

EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation

Nathan C Frey, A. Regev, Payman Yadollahpour, 2023, bioRxiv.

Predicting protein structures with a multiplayer online game

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

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Brian D. Weitzner, Karen R. Khar, Roland L. Dunbrack, 2020, Nature Methods.

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.

Computational design of a specific heavy chain/κ light chain interface for expressing fully IgG bispecific antibodies

B. Kuhlman, B. Kuhlman, Xiufeng Wu, 2017, Protein science : a publication of the Protein Society.

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

Jack Snoeyink, Andrew Leaver-Fay, Xueyi Wang, 2007, Nucleic Acids Res..

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

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

Role of conformational sampling in computing mutation‐induced changes in protein structure and stability

D. Baker, A. Leaver-Fay, E. Kellogg, 2011, Proteins.

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

Jason W. Labonte, Jeffrey J. Gray, Johanna K. S. Tiemann, 2021, Nature Communications.

Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta.

Matthew J. O’Meara, P. Bradley, D. Baker, 2015, Journal of chemical theory and computation.

Rotamer-Pair Energy Calculations Using a Trie Data Structure

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

Capturing atomic interactions with a graphical framework in computational protein design

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

De Novo Enzyme Design Using Rosetta3

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

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

Vincent B. Chen, Ian W. Davis, Jeremy N. Block, 2007 .

Computational protein design with explicit consideration of surface hydrophobic patches

B. Kuhlman, A. Leaver-Fay, Ron Jacak, 2012, Proteins.

The challenge of designing scientific discovery games

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

Computationally Designed Bispecific Antibodies using Negative State Repertoires.

B. Kuhlman, A. Leaver-Fay, S. Atwell, 2016, Structure.

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

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

Computational design of a PAK1 binding protein.

Shuangye Yin, B. Kuhlman, N. Dokholyan, 2010, Journal of Molecular Biology.

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

Oliver F. Lange, Jeffrey J. Gray, Ian W. Davis, 2011, Methods in enzymology.

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

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

A Generic Program for Multistate Protein Design

Andrew Leaver-Fay, Brian Kuhlman, Ron Jacak, 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..

RosettaTMH: a method for membrane protein structure elucidation combining EPR distance restraints with assembly of transmembrane helices

Samuel L. DeLuca, A. Leaver-Fay, J. Meiler, 2015 .

SwiftLib: rapid degenerate-codon-library optimization through dynamic programming

B. Kuhlman, A. Leaver-Fay, H. Yumerefendi, 2014, Nucleic acids research.

Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design

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

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

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

An Adaptive Dynamic Programming Algorithm for the Side Chain Placement Problem

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

Maintaining solvent accessible surface area under rotamer substitution for protein design

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