Brian Kuhlman

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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.

RosettaDesign server for protein design

Yi Liu, Brian Kuhlman, B. Kuhlman, 2006, Nucleic Acids Res..

Protocols for Requirement-Driven Protein Design in the Rosetta Modeling Program

Brian Kuhlman, Sharon L Guffy, Frank D Teets, 2018, J. Chem. Inf. Model..

Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design

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

Engineering Improved Photoswitches for the Control of Nucleocytoplasmic Distribution.

Brian Kuhlman, Andrew M Lerner, Hayretin Yumerefendi, 2018, ACS synthetic biology.

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design.

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

Typical development workflow in the Rosetta community.

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

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..

Advances in protein structure prediction and design

Brian Kuhlman, Philip Bradley, P. Bradley, 2019, Nature Reviews Molecular Cell Biology.

UbSRD: The Ubiquitin Structural Relational Database.

Brian Kuhlman, Joseph S Harrison, Tim M Jacobs, 2016, Journal of molecular biology.

Investigation of test methods for DO-160 qualification tests

Brian Kuhlman, Taosong He, 2003, 2003 IEEE Symposium on Electromagnetic Compatibility. Symposium Record (Cat. No.03CH37446).

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

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

Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design.

Brian Kuhlman, David Baker, Jack B. Maguire, 2018, Journal of chemical theory and computation.

Growth in Rosetta PIs and conference attendees.

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

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..

Commercial spin-off companies from the Rosetta community.

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

Effects of Aircraft Interaction on Performance of B-Dot Sensor for Delta-Wing and Cargo-Type Aircraft.

Valdis Vincents Liepa, Brian Kuhlman, Arturo Serano, 1986 .

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.

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 .

Future Challenges Of Computational Protein Design

Brian Kuhlman, Eun Jung Choi, Gurkan Guntas, 2009 .

Designing protein structures and complexes with the molecular modeling program Rosetta

Brian Kuhlman, B. Kuhlman, 2019, The Journal of Biological Chemistry.

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design

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

Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins

Brian Kuhlman, James E Bear, Hayretin Yumerefendi, 2014, Proceedings of the National Academy of Sciences.

Light-induced nuclear export reveals rapid dynamics of epigenetic modifications

Brian Kuhlman, Brian D. Strahl, James E Bear, 2016, Nature chemical biology.

From Computational Design to a Protein That Binds

Brian Kuhlman, Bryan S. Der, B. Kuhlman, 2011, Science.

Computational design of the sequence and structure of a protein-binding peptide.

Brian Kuhlman, Glenn L. Butterfoss, David P. Siderovski, 2011, Journal of the American Chemical Society.

Metal templated design of protein interfaces

Brian Kuhlman, Richard A. Lewis, B. Kuhlman, 2009, Proceedings of the National Academy of Sciences.

Designing photoswitchable peptides using the AsLOV2 domain.

Brian Kuhlman, Eun Jung Choi, Klaus M Hahn, 2012, Chemistry & biology.

Catalysis by a de novo zinc-mediated protein interface: implications for natural enzyme evolution and rational enzyme engineering.

Brian Kuhlman, Bryan S. Der, Bryan S Der, 2012, Biochemistry.

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

Sergey Lyskov, Brian Kuhlman, Jeffrey J. Gray, 2013, PloS one.

Computer-based redesign of a protein folding pathway

David Baker, Brian Kuhlman, D. Baker, 2001, Nature Structural Biology.

A Generic Program for Multistate Protein Design

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

Boosting protein stability with the computational design of β‐sheet surfaces

Brian Kuhlman, Doo Nam Kim, B. Kuhlman, 2016, Protein science : a publication of the Protein Society.

PROTEINS: Structure, Function, and Bioinformatics 58:893–904 (2005) A “Solvated Rotamer ” Approach to Modeling Water- Mediated Hydrogen Bonds at Protein–Protein Interfaces

David Baker, Tanja Kortemme, Brian Kuhlman, 2022 .

Cells lay their own tracks – optogenetic Cdc42 activation stimulates fibronectin deposition supporting directed migration

Brian Kuhlman, B. Kuhlman, S. Zimmerman, 2017, Journal of Cell Science.

E2 conjugating enzymes must disengage from their E1 enzymes before E3-dependent ubiquitin and ubiquitin-like transfer

Brian Kuhlman, B. Kuhlman, Ziad M. Eletr, 2005, Nature Structural &Molecular Biology.

High-resolution design of a protein loop

Brian Kuhlman, Xiaozhen Hu, Xiaozhen Hu, 2007, Proceedings of the National Academy of Sciences.

Fab-based bispecific antibody formats with robust biophysical properties and biological activity

Brian Kuhlman, Steven M Lewis, Xiufeng Wu, 2015, mAbs.

Correlating in Vitro and in Vivo Activities of Light-Inducible Dimers: A Cellular Optogenetics Guide.

Brian Kuhlman, James E Bear, Hayretin Yumerefendi, 2016, ACS synthetic biology.

Protein design simulations suggest that side‐chain conformational entropy is not a strong determinant of amino acid environmental preferences

Brian Kuhlman, Xiaozhen Hu, Xiaozhen Hu, 2005, Proteins.

A preliminary survey of the peptoid folding landscape.

Richard Bonneau, Brian Kuhlman, Kent Kirshenbaum, 2009, Journal of the American Chemical Society.

Using anchoring motifs for the computational design of protein-protein interactions.

Brian Kuhlman, B. Kuhlman, T. Jacobs, 2013, Biochemical Society transactions.

Computational design of a PAK1 binding protein.

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

Rapid E2-E3 Assembly and Disassembly Enable Processive Ubiquitylation of Cullin-RING Ubiquitin Ligase Substrates

Brian Kuhlman, Steven Lewis, Raymond J. Deshaies, 2009, Cell.

Computational design of second‐site suppressor mutations at protein–protein interfaces

Brian Kuhlman, B. Kuhlman, D. Sammond, 2010, Proteins.

Minimal determinants for binding activated G alpha from the structure of a G alpha(i1)-peptide dimer.

Brian Kuhlman, Vadim Y Arshavsky, Alexander S Shavkunov, 2006, Biochemistry.

Strategies to control the binding mode of de novo designed protein interactions.

Brian Kuhlman, Bryan S. Der, Bryan S Der, 2013, Current opinion in structural biology.

LOVTRAP, An Optogenetic System for Photo-induced Protein Dissociation

Gaudenz Danuser, Brian Kuhlman, Andreas Winkler, 2016, Nature Methods.

Computational design of a symmetric homodimer using β-strand assembly

Brian Kuhlman, Ashutosh Tripathy, B. Kuhlman, 2011, Proceedings of the National Academy of Sciences.

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.

Computer-based design of novel protein structures.

Brian Kuhlman, Glenn L Butterfoss, B. Kuhlman, 2006, Annual review of biophysics and biomolecular structure.

Go in! Go out! Inducible control of nuclear localization.

Brian Kuhlman, B. Kuhlman, B. Di Ventura, 2016, Current opinion in chemical biology.

Computational de novo design of a four‐helix bundle protein—DND_4HB

Thomas Szyperski, Brian Kuhlman, Bryan S. Der, 2015, Protein science : a publication of the Protein Society.

Structure-based design of supercharged, highly thermoresistant antibodies.

Brian Kuhlman, Jeffrey J. Gray, George Georgiou, 2012, Chemistry & biology.

Engineering a protein–protein interface using a computationally designed library

Brian Kuhlman, Gurkan Guntas, B. Kuhlman, 2010, Proceedings of the National Academy of Sciences.

Exploring folding free energy landscapes using computational protein design.

David Baker, Brian Kuhlman, D. Baker, 2004, Current opinion in structural biology.

Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2

David Baker, Brian Kuhlman, David Teller, 2002 .

Data in support of UbSRD: The Ubiquitin Structural Relational Database

Brian Kuhlman, Kevin Houlihan, Koenraad Van Doorslaer, 2015, Data in brief.

Erratum: Designing photoswitchable peptides using the AsLOV2 domain (Chemistry and Biology (2012) 19 (507-517))

Brian Kuhlman, Eun Jung Choi, B. Kuhlman, 2012 .

Computational Repacking of HIF-2α Cavity Replaces Water-Based Stabilized Core.

Brian Kuhlman, B. Kuhlman, K. Gardner, 2016, Structure.

Cages from coils

Brian Kuhlman, Bryan S Der, 2013, Nature Biotechnology.

A computational protocol for regulating protein binding reactions with a light sensitive protein dimer.

Brian Kuhlman, Frank D. Teets, B. Kuhlman, 2019, Journal of molecular biology.

Design of protein conformational switches.

Brian Kuhlman, B. Kuhlman, X. Ambroggio, 2006, Current opinion in structural biology.

Sequence determinants of E2-E6AP binding affinity and specificity.

Brian Kuhlman, B. Kuhlman, Ziad M. Eletr, 2007, Journal of molecular biology.