B. Kuhlman

发表

Design of a Novel Globular Protein Fold with Atomic-Level Accuracy

D. Baker, B. Stoddard, B. Kuhlman, 2003, Science.

Labelling and optical erasure of synaptic memory traces in the motor cortex

Amanda L. Loshbaugh, Sho Yagishita, A. Hayashi‐Takagi, 2015, Nature.

An improved protein decoy set for testing energy functions for protein structure prediction

Richard Bonneau, D. Baker, J. Tsai, 2003, Proteins.

Computational design of a single amino acid sequence that can switch between two distinct protein folds.

B. Kuhlman, X. Ambroggio, 2006, Journal of the American Chemical Society.

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

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

Native protein sequences are close to optimal for their structures.

D. Baker, B. Kuhlman, David Baker, 2000, Proceedings of the National Academy of Sciences of the United States of America.

Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer.

Bryan S. Der, B. Kuhlman, T. Szyperski, 2012, Journal of the American Chemical Society.

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.

Jeffrey J. Gray, Stewart E. Moughon, O. Schueler‐Furman, 2003, Journal of molecular biology.

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.

Accurate computer-based design of a new backbone conformation in the second turn of protein L.

Kam Y. J. Zhang, David E. Kim, D. Baker, 2002, Journal of molecular biology.

A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds

B. Kuhlman, P. B. Stranges, 2013, Protein science : a publication of the Protein Society.

Computational protein design with explicit consideration of surface hydrophobic patches

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

Anchored Design of Protein-Protein Interfaces

Steven M. Lewis, B. Kuhlman, 2011, PloS one.

Incorporation of Noncanonical Amino Acids into Rosetta and Use in Computational Protein-Peptide Interface Design

Eun Jung Choi, Richard Bonneau, B. Kuhlman, 2012, PloS one.

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

Brian D. Weitzner, Jeffrey J. Gray, Bryan S. Der, 2013, PloS one.

Increasing sequence diversity with flexible backbone protein design: the complete redesign of a protein hydrophobic core.

B. Kuhlman, T. Szyperski, M. Machius, 2012, Structure.

Computer-based redesign of a beta sandwich protein suggests that extensive negative design is not required for de novo beta sheet design.

Xiaozhen Hu, B. Kuhlman, H. Ke, 2008, Structure.

High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design

D. Baker, B. Kuhlman, G. Dantas, 2007, Journal of molecular biology.

Computational design of affinity and specificity at protein-protein interfaces.

B. Kuhlman, J. Karanicolas, 2009, Current opinion in structural biology.

A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins.

D. Baker, B. Kuhlman, G. Dantas, 2003, Journal of molecular biology.

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

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

Using quantum mechanics to improve estimates of amino acid side chain rotamer energies

B. Kuhlman, P. D. Renfrew, G. L. Butterfoss, 2007, Proteins.

Computational design of a symmetric homodimer using β-strand assembly

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

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 .

Sequence determinants of E2-E6AP binding affinity and specificity.

Brian Kuhlman, B. Kuhlman, Ziad M. Eletr, 2007, 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.

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.

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.

Role of electrostatic repulsion in controlling pH-dependent conformational changes of viral fusion proteins.

Matthew J. O’Meara, B. Kuhlman, J. Lai, 2013, Structure.

Control of Protein Activity and Cell Fate Specification via Light-Mediated Nuclear Translocation

B. Kuhlman, K. Hahn, H. Yumerefendi, 2015, PloS one.

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

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

Design of protein conformational switches.

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

Global analysis of the effects of temperature and denaturant on the folding and unfolding kinetics of the N-terminal domain of the protein L9.

B. Kuhlman, D. Raleigh, D. Luisi, 1998, Journal of molecular biology.

A genetically-encoded photoactivatable Rac controls the motility of living cells

B. Kuhlman, Yi I. Wu, K. Hahn, 2009, Nature.

Structure-based protocol for identifying mutations that enhance protein-protein binding affinities.

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

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

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

Structure-based design of supercharged, highly thermoresistant antibodies.

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

Exploring folding free energy landscapes using computational protein design.

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

Conversion of monomeric protein L to an obligate dimer by computational protein design

Kam Y. J. Zhang, D Baker, David E. Kim, 2001, Proceedings of the National Academy of Sciences of the United States of America.

Structural Insights into Thioether Bond Formation in the Biosynthesis of Sactipeptides.

B. Kuhlman, S. Almo, J. Bonanno, 2017, Journal of the American Chemical Society.

The Rodin-Ohno hypothesis that two enzyme superfamilies descended from one ancestral gene: an unlikely scenario for the origins of translation that will not be dismissed

B. Kuhlman, C. Carter, X. Ambroggio, 2014, Biology Direct.

Mechanism of Lysine 48 Selectivity during Polyubiquitin Chain Formation by the Ube2R1/2 Ubiquitin-Conjugating Enzyme

Steven M. Lewis, B. Kuhlman, G. Kleiger, 2016, Molecular and Cellular Biology.

Folding of the multidomain ribosomal protein L9: the two domains fold independently with remarkably different rates.

B. Kuhlman, D. Raleigh, S. Sato, 1999, Biochemistry.

From Computational Design to a Protein That Binds

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

Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution.

D. Baker, B. Stoddard, B. Kuhlman, 2006, Journal of molecular 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.

Designing protein structures and complexes with the molecular modeling program Rosetta

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

Light-induced nuclear export reveals rapid dynamics of epigenetic modifications

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

Light‐Dependent Cytoplasmic Recruitment Enhances the Dynamic Range of a Nuclear Import Photoswitch

B. Kuhlman, K. Hahn, H. Yumerefendi, 2018, Chembiochem : a European journal of chemical biology.

Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1

B. Kuhlman, B. Strahl, C. Arrowsmith, 2016, eLife.

Design and engineering of light-sensitive protein switches.

B. Kuhlman, Amelia C. McCue, 2022, Current opinion in structural biology.

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 .

Commercial spin-off companies from the Rosetta community.

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

A Bifunctional Role for the UHRF1 UBL Domain in the Control of Hemi-methylated DNA-Dependent Histone Ubiquitylation.

B. Kuhlman, T. Davis, P. Brzovic, 2018, Molecular cell.

Advances in Modular Control of CAR-T Therapy with Adapter-Mediated CARs.

B. Kuhlman, Amelia C. McCue, Zhiyuan Yao, 2022, Advanced drug delivery reviews.

Functional Class I and II amino acid-activating enzymes can be coded by opposite strands of the same gene.

B. Kuhlman, C. Carter, X. Ambroggio, 2016, The Journal of Biological Chemistry.

A conformational transition state accompanies tryptophan activation by B. stearothermophilus tryptophanyl-tRNA synthetase.

B. Kuhlman, C. Carter, M. Kapustina, 2007, Structure.

We FRET so You Don't Have To: New Models of the Lipoprotein Lipase Dimer.

B. Kuhlman, S. Neher, D. Erie, 2018, Biochemistry.

Computer-based Redesign of a β-Sandwich Protein Suggests that Extensive Negative Design is Not Required for De Novo β-Sheet Design

Xiaozhen Hu, B. Kuhlman, H. Ke, 2009 .

Computational stabilization of T cell receptors allows pairing with antibodies to form bispecifics

Jack B. Maguire, B. Kuhlman, Xiufeng Wu, 2020, Nature Communications.

Computer-based Engineering of Thermostabilized Antibody Fragments.

Jeffrey J. Gray, R. A. Hughes, Bryan S. Der, 2019, AIChE journal. American Institute of Chemical Engineers.

Modifications to the Framework Regions Eliminate Chimeric Antigen Receptor Tonic Signaling

B. Kuhlman, N. Dokholyan, G. Finocchiaro, 2021, Cancer Immunology Research.

Lamellipodia are crucial for haptotactic sensing and response

B. Kuhlman, N. Sharpless, J. Haugh, 2016, Journal of Cell Science.

Details of Remaining Collective Challenges.

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

Members of the RosettaCommons Consortium.

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

Growth in Rosetta PIs and conference attendees.

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

Perturbing the energy landscape for improved packing during computational protein design

Jack B. Maguire, Jermel R. Griffin, Jermel R Griffin, 2020, Proteins.

Control of microtubule dynamics using an optogenetic microtubule plus end–F-actin cross-linker

B. Kuhlman, K. Slep, Ryan A. Hallett, 2017, bioRxiv.

Designer installation of a substrate recruitment domain to tailor enzyme specificity

B. Kuhlman, S. Nair, C. Ongpipattanakul, 2022, Nature Chemical Biology.

Tryptophanyl-tRNA Synthetase Urzyme

B. Kuhlman, C. Carter, G. L. Butterfoss, 2010, The Journal of Biological Chemistry.

Requirements for 5′dRP/AP lyase activity in Ku

B. Kuhlman, D. Ramsden, N. Strande, 2014, Nucleic acids research.

Erratum: Native protein sequences are close to optimal for their structures (Proceedings of the National Academy of Sciences of the United States of America (September 12, 2000) 97 (10383-10388))

D. Baker, B. Kuhlman, 2000 .

Evolution of a highly active and enantiospecific metalloenzyme from short peptides

Bryan S. Der, B. Kuhlman, D. Hilvert, 2018, Science.

A preliminary survey of the peptoid folding landscape.

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

Design of structurally distinct proteins using strategies inspired by evolution

B. Kuhlman, T. Szyperski, B. Kuhlman, 2016, Science.

Global analysis of the thermal and chemical denaturation of the N‐terminal domain of the ribosomal protein L9 in H2O and D2O. Determination of the thermodynamic parameters, ΔH°, ΔS°, and ΔC°p, and evaluation of solvent isotope effects

B. Kuhlman, D. Raleigh, 1998 .

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

D. Baker, B. Kuhlman, D. Teller, 2002, Protein science : a publication of the Protein Society.

Metal templated design of protein interfaces

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

Designed, highly expressing, thermostable dengue virus 2 envelope protein dimers elicit quaternary epitope antibodies

Jack B. Maguire, B. Kuhlman, Gregory D. Gromowski, 2021, Science advances.

Dimerization of Dengue Virus E Subunits Impacts Antibody Function and Domain Focus

B. Kuhlman, L. Premkumar, A. D. de Silva, 2020, Journal of Virology.

Physiological temperatures reduce dimerization of dengue and Zika virus recombinant envelope proteins

B. Kuhlman, M. Miley, A. Bobkov, 2018, The Journal of Biological Chemistry.

An exceptionally stable helix from the ribosomal protein L9: implications for protein folding and stability.

B. Kuhlman, D. Raleigh, R. Fairman, 1997, Journal of molecular biology.

Probing the minimal determinants of zinc binding with computational protein design.

Bryan S. Der, B. Kuhlman, Sharon L. Guffy, 2016, Protein engineering, design & selection : PEDS.

Comparative biochemical analysis of UHRF proteins reveals molecular mechanisms that uncouple UHRF2 from DNA methylation maintenance

B. Kuhlman, B. Dickson, J. Harrison, 2018, Nucleic acids research.

Optogenetic control of Cofilin and αTAT in living cells using Z-lock

Frank D. Teets, B. Kuhlman, K. Hahn, 2019, Nature Chemical Biology.

Advances in protein structure prediction and design

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

Computational design of a PAK1 binding protein.

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

Biophysical and structural characterization of novel RAS-binding domains (RBDs) of PI3Kα and PI3Kγ.

B. Kuhlman, David F. Thieker, S. Campbell, 2021, Journal of molecular biology.

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

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

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.

Glutamine Triggers Acetylation-Dependent Degradation of Glutamine Synthetase via the Thalidomide Receptor Cereblon.

Justin M. Reitsma, Michael J. Sweredoski, B. Kuhlman, 2016, Molecular cell.

LOVTRAP, An Optogenetic System for Photo-induced Protein Dissociation

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

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.

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

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

Site–Specific Monoubiquitination Activates Ras by Impeding GTPase Activating Protein Function

Steven M. Lewis, B. Kuhlman, H. Dohlman, 2012, Nature Structural &Molecular Biology.

Ras has a central role in cell growth, differentiation and apoptosis and is a member of a large superfamily of guanine nucleotide–binding

Steven M. Lewis, B. Kuhlman, H. Dohlman, 2012 .

A biosensor generated via high throughput screening quantifies cell edge Src dynamics

Steven M. Lewis, Eric A. Vitriol, T. Elston, 2011, Nature chemical biology.

Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design.

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

Scientific benchmarks for guiding macromolecular energy function improvement.

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

RosettaDesign server for protein design

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

Macromolecular modeling and design in Rosetta: recent methods and frameworks

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

An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation

B. Kuhlman, B. Strahl, I. Davis, 2020, bioRxiv.

A structural bioinformatics approach for identifying proteins predisposed to bind linear epitopes on pre-selected target proteins.

Eun Jung Choi, B. Kuhlman, Ron Jacak, 2013, Protein engineering, design & selection : PEDS.

Design of a protease‐activated PD‐L1 inhibitor

Odessa J Goudy, B. Kuhlman, A. Tripathy, 2023, Protein science : a publication of the Protein Society.

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

Kengo Kinoshita, Haruki Nakamura, Genki Terashi, 2011, Journal of molecular biology.

Engineering Improved Photoswitches for the Control of Nucleocytoplasmic Distribution.

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

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.

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

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

Ubiquitin-conjugating Enzyme Cdc34 and Ubiquitin Ligase Skp1-Cullin-F-box Ligase (SCF) Interact through Multiple Conformations*

Steven M. Lewis, B. Kuhlman, G. Kleiger, 2014, The Journal of Biological Chemistry.

AlphaFold accurately predicts distinct conformations based on oligomeric state of a de novo designed protein

Frank D. Teets, B. Kuhlman, A. Tripathy, 2022, bioRxiv.

Designer proteins that competitively inhibit Gαq by targeting its effector site

B. Kuhlman, J. Sondek, S. Endo-Streeter, 2021, The Journal of biological chemistry.

Functional Class I and II Amino Acid-activating Enzymes Can Be Coded by Opposite Strands of the Same Gene*

B. Kuhlman, C. Carter, X. Ambroggio, 2015, The Journal of Biological Chemistry.

Cooperative folding of a protein mini domain: the peripheral subunit-binding domain of the pyruvate dehydrogenase multienzyme complex.

B. Kuhlman, D. Raleigh, R. Fairman, 1998, Journal of molecular biology.

Stabilizing proteins, simplified: A Rosetta‐based webtool for predicting favorable mutations

Jack B. Maguire, B. Kuhlman, A. Leaver-Fay, 2022, Protein science : a publication of the Protein Society.

NEW APPROACHES FOR CONTROL AND VISUALIZATION OF PROTEIN CONFORMATION IN LIVE CELLS

T. Elston, B. Kuhlman, K. Hahn, 2018 .

Computational stabilization of T cell receptors allows pairing with antibodies to form bispecifics

Jack B. Maguire, B. Kuhlman, Xiufeng Wu, 2020, Nature Communications.

USING AUREOCHROME TO CONTROL PROTEIN-PROTEIN INTERA CTIONS WITH LIGHT

B. Kuhlman, Gary L. Johnson, Yi Wu, 2012 .

Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C

B. Kuhlman, M. Kirschner, J. Peters, 2016, Cell.

Dual RING E 3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC / C Graphical

B. Kuhlman, M. Kirschner, J. Peters, 2022 .

Computer-based design of novel protein structures.

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

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

David Baker, Brian Kuhlman, David Teller, 2002 .

Computer-based redesign of a protein folding pathway

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

G Protein Mono-ubiquitination by the Rsp 5 Ubiquitin Ligase *

B. Kuhlman, H. Dohlman, Michael J. Lee, 2009 .

Maintaining solvent accessible surface area under rotamer substitution for protein design

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

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.

Combined computational design of a zinc‐binding site and a protein–protein interaction: One open zinc coordination site was not a robust hotspot for de novo ubiquitin binding

Steven M. Lewis, Bryan S. Der, B. Kuhlman, 2013, Proteins.

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design.

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

Rotamer-Pair Energy Calculations Using a Trie Data Structure

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

Redesigning the NEDD8 pathway with a bacterial genetic screen for ubiquitin-like molecule transfer.

B. Kuhlman, Gurkan Guntas, 2012, Journal of molecular biology.

Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3

Steven M. Lewis, B. Kuhlman, B. Schulman, 2013, eLife.

Designing photoswitchable peptides using the AsLOV2 domain.

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

High-resolution design of a protein loop

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

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

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

Engineering a Protein Binder Specific for p38α with Interface Expansion.

B. Kuhlman, S. Angus, Mahmud M. Hussain, 2018, Biochemistry.

Erratum to Originally published in PROTEINS: Structure, Function, and Bioinformatics [81(7), (2013), 1245-1255] DOI:10.1002/prot.24280

Steven M. Lewis, Bryan S. Der, B. Kuhlman, 2013 .

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.

A minimal TrpRS catalytic domain supports sense/antisense ancestry of class I and II aminoacyl-tRNA synthetases.

B. Kuhlman, C. Carter, G. L. Butterfoss, 2007, Molecular cell.

Engineering and Application of LOV2-Based Photoswitches.

B. Kuhlman, H. Yumerefendi, S. Zimmerman, 2016, Methods in enzymology.

From Protein Design to the Energy Landscape of a Cold Unfolding Protein

Jack B. Maguire, Jermel R. Griffin, Surya V. S. R. K. Pulavarti, 2022, The journal of physical chemistry. B.

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.

Engineering a protein–protein interface using a computationally designed library

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

Computationally Designed Bispecific Antibodies using Negative State Repertoires.

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

Essential role for ubiquitin-ubiquitin-conjugating enzyme interaction in ubiquitin discharge from Cdc34 to substrate.

Steven M. Lewis, B. Kuhlman, Anjanabha Saha, 2011, Molecular cell.

Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design

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

An Adaptive Dynamic Programming Algorithm for the Side Chain Placement Problem

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

Redesign of the PAK1 autoinhibitory domain for enhanced stability and affinity in biosensor applications.

B. Kuhlman, Yi I. Wu, K. Hahn, 2011, Journal of molecular biology.

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.

De novo design of stable proteins that efficaciously inhibit oncogenic G proteins

B. Kuhlman, J. Sondek, A. Tripathy, 2023, bioRxiv.

Structure and stability of the N-terminal domain of the ribosomal protein L9: evidence for rapid two-state folding.

B. Kuhlman, D. Raleigh, R. Fairman, 1998, Biochemistry.

Engineering a genetically encoded competitive inhibitor of the KEAP1-NRF2 interaction via structure-based design and phage display.

Steven M. Lewis, B. Kuhlman, Gurkan Guntas, 2015, Protein engineering, design & selection : PEDS.

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

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

A Generic Program for Multistate Protein Design

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

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

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

A conserved set of mutations for stabilizing soluble envelope protein dimers from dengue and Zika viruses to advance the development of subunit vaccines

B. Kuhlman, A. Tripathy, N. Nicely, 2022, The Journal of biological chemistry.

Calcium binding peptides from alpha-lactalbumin: implications for protein folding and stability.

B. Kuhlman, D. Raleigh, R. Fairman, 1997, Biochemistry.

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.

Tuning the Binding Affinities and Reversion Kinetics of a Light Inducible Dimer Allows Control of Transmembrane Protein Localization.

B. Kuhlman, S. Zimmerman, J. Bear, 2016, Biochemistry.

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.

Supertertiary structure of the MAGUK core from PSD-95.

Andrew L. Lee, Steven M. Lewis, B. Kuhlman, 2013, Structure.

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..

Computational design of a PAK1 binding protein.

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

Macromolecular modeling and design in Rosetta: recent methods and frameworks

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

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.

Kinetics of the transfer of ubiquitin from UbcH7 to E6AP.

B. Kuhlman, Ziad M. Eletr, Carrie Purbeck, 2010, Biochemistry.

Future Challenges Of Computational Protein Design

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

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

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

In silico evolution of protein binders with deep learning models for structure prediction and sequence design

Odessa J Goudy, Nicholas Z Randolph, B. Kuhlman, 2023, bioRxiv.

Transfer learning to leverage larger datasets for improved prediction of protein stability changes

Nicholas Z Randolph, B. Kuhlman, Henry Dieckhaus, 2023, bioRxiv.

Hold me tightly LOV

B. Kuhlman, K. Hahn, 2010, Nature Methods.

Invariant point message passing for protein side chain packing

Nicholas Z Randolph, B. Kuhlman, Nicholas Randolph, 2023, bioRxiv.

De novo design of stable proteins that efficaciously inhibit oncogenic G proteins

B. Kuhlman, J. Sondek, A. Tripathy, 2023, Protein science : a publication of the Protein Society.

Inside-Out Design of Zinc-Binding Proteins with Non-Native Backbones.

Surya V. S. R. K. Pulavarti, B. Kuhlman, T. Szyperski, 2023, Biochemistry.

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

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

G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase*

B. Kuhlman, H. Dohlman, Michael J. Lee, 2009, Journal of Biological Chemistry.

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

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

Lamellipodia are crucial for haptotactic sensing and response

B. Kuhlman, N. Sharpless, J. Haugh, 2016, Journal of Cell Science.

Computational design of a symmetric homodimer using β-strand assembly

B. Kuhlman, P. B. Stranges, M. Machius, 2011, Proceedings of the National Academy of Sciences.

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

Bryan S. Der, Surya V. S. R. K. Pulavarti, B. Kuhlman, 2015, Protein science : a publication of the Protein Society.

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

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

A structural bioinformatics approach for identifying proteins predisposed to bind linear epitopes on pre-selected target proteins.

Eun Jung Choi, B. Kuhlman, Ron Jacak, 2013, Protein engineering, design & selection : PEDS.

A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds

B. Kuhlman, P. B. Stranges, 2013, Protein science : a publication of the Protein Society.

Computational design of a PAK1 binding protein.

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

Computational design of affinity and specificity at protein-protein interfaces.

B. Kuhlman, J. Karanicolas, 2009, Current opinion in structural 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.

Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer.

Bryan S. Der, B. Kuhlman, T. Szyperski, 2012, Journal of the American Chemical Society.

Designing photoswitchable peptides using the AsLOV2 domain.

Eun Jung Choi, B. Kuhlman, K. Hahn, 2012, Chemistry & biology.

Computer-based redesign of a beta sandwich protein suggests that extensive negative design is not required for de novo beta sheet design.

Xiaozhen Hu, B. Kuhlman, H. Ke, 2008, Structure.

Structure-based design of supercharged, highly thermoresistant antibodies.

Jeffrey J. Gray, Alena M Calm, Bryan S. Der, 2012, Chemistry & biology.

Mechanism of Lysine 48 Selectivity during Polyubiquitin Chain Formation by the Ube2R1/2 Ubiquitin-Conjugating Enzyme

Steven M. Lewis, B. Kuhlman, J. Harrison, 2016, Molecular and Cellular Biology.

Data in support of UbSRD: The Ubiquitin Structural Relational Database

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

Site-specific monoubiquitination activates Ras by impeding GTPase-activating protein function

Steven M. Lewis, B. Kuhlman, H. Dohlman, 2013, Small GTPases.

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

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

Structural Determinants of Affinity Enhancement between GoLoco Motifs and G-Protein α Subunit Mutants*

B. Kuhlman, D. Sammond, M. Machius, 2010, The Journal of Biological Chemistry.

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

B. Kuhlman, D. Sammond, Ziad M. Eletr, 2010, Proteins.

pKa values and the pH dependent stability of the N-terminal domain of L9 as probes of electrostatic interactions in the denatured state. Differentiation between local and nonlocal interactions.

B. Kuhlman, D. Raleigh, P. Young, 1999, Biochemistry.

A biosensor generated via high throughput screening quantifies cell edge Src dynamics

Steven M. Lewis, Eric A. Vitriol, T. Elston, 2011, Nature chemical biology.

Correction: Corrigendum: A biosensor generated via high-throughput screening quantifies cell edge Src dynamics

Steven M. Lewis, Eric A. Vitriol, T. Elston, 2012 .

G Protein Mono-ubiquitination by the Rsp5 Ubiquitin Ligase*

B. Kuhlman, H. Dohlman, Michael J. Lee, 2009, Journal of Biological Chemistry.

Invariant point message passing for protein side chain packing

Nicholas Z Randolph, B. Kuhlman, 2023, bioRxiv.

A Bifunctional Role for the UHRF1 UBL Domain in the Control of Hemi-methylated DNA-Dependent Histone Ubiquitylation.

B. Kuhlman, T. Davis, P. Brzovic, 2018, Molecular cell.

Effects of varying the local propensity to form secondary structure on the stability and folding kinetics of a rapid folding mixed alpha/beta protein: characterization of a truncation mutant of the N-terminal domain of the ribosomal protein L9.

B. Kuhlman, D. Raleigh, D. Luisi, 1999, Journal of Molecular Biology.

Global analysis of the thermal and chemical denaturation of the N-terminal domain of the ribosomal protein L9 in H2O and D2O. Determination of the thermodynamic parameters, deltaH(o), deltaS(o), and deltaC(o)p and evaluation of solvent isotope effects.

B. Kuhlman, D. Raleigh, 1998, Protein science : a publication of the Protein Society.