Brian Kuhlman

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 57

Top Topics

Protein Protein

Top Venues

bioRxiv : the preprint server for biology

Protein science : a publication of the Protein Society

Proceedings of the National Academy of Sciences of the United States of America

This page only lists publications with an associated author ORCID identifier.

Publications

Henry Dieckhaus, Michael Brocidiacono, Nicholas Z Randolph, Brian Kuhlman
Transfer learning to leverage larger datasets for improved prediction of protein stability changes. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Henry Dieckhaus, Michael Brocidiacono, Nicholas Z Randolph, Brian Kuhlman
Transfer learning to leverage larger datasets for improved prediction of protein stability changes. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Henry Dieckhaus, Michael Brocidiacono, Nicholas Z Randolph, Brian Kuhlman
Transfer learning to leverage larger datasets for improved prediction of protein stability changes. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Henry Dieckhaus, Brian Kuhlman
Protein stability models fail to capture epistatic interactions of double point mutations. bioRxiv : the preprint server for biology (2024)
Henry Dieckhaus, Michael Brocidiacono, Nicholas Z Randolph, Brian Kuhlman
Transfer learning to leverage larger datasets for improved prediction of protein stability changes. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Amelia C McCue, Stephen J Demarest, Karen J Froning, Michael J Hickey, Stephen Antonysamy, Brian Kuhlman
Engineering a tumor-selective prodrug T-cell engager bispecific antibody for safer immunotherapy. mAbs 16 (1) (2024)
Henry Dieckhaus, Michael Brocidiacono, Nicholas Z Randolph, Brian Kuhlman
Transfer learning to leverage larger datasets for improved prediction of protein stability changes. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Nicholas Z Randolph, Brian Kuhlman
Invariant point message passing for protein side chain packing. Proteins (2024)
Henry Dieckhaus, Michael Brocidiacono, Nicholas Z Randolph, Brian Kuhlman
Transfer learning to leverage larger datasets for improved prediction of protein stability changes. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Nicholas Z Randolph, Brian Kuhlman
Invariant point message passing for protein side chain packing. Proteins (2024)
Amelia C McCue, Stephen J Demarest, Karen J Froning, Michael J Hickey, Stephen Antonysamy, Brian Kuhlman
Engineering a tumor-selective prodrug T-cell engager bispecific antibody for safer immunotherapy. mAbs 16 (1) (2024)
Amelia C McCue, Stephen J Demarest, Karen J Froning, Michael J Hickey, Stephen Antonysamy, Brian Kuhlman
Engineering a tumor-selective prodrug T-cell engager bispecific antibody for safer immunotherapy. mAbs 16 (1) (2024)
Henry Dieckhaus, Michael Brocidiacono, Nicholas Z Randolph, Brian Kuhlman
Transfer learning to leverage larger datasets for improved prediction of protein stability changes. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Odessa J Goudy, Alice Peng, Ashutosh Tripathy, Brian Kuhlman
Design of a protease-activated PD-L1 inhibitor. Protein science : a publication of the Protein Society (2023)
Odessa J Goudy, Alice Peng, Ashutosh Tripathy, Brian Kuhlman
Design of a protease-activated PD-L1 inhibitor. Protein science : a publication of the Protein Society (2023)
Matthew C Cummins, Ashutosh Tripathy, John Sondek, Brian Kuhlman
De novo design of stable proteins that efficaciously inhibit oncogenic G proteins. bioRxiv : the preprint server for biology (2023)
Odessa J Goudy, Amrita Nallathambi, Tomoaki Kinjo, Nicholas Z Randolph, Brian Kuhlman
In silico evolution of protein binders with deep learning models for structure prediction and sequence design. bioRxiv : the preprint server for biology (2023)
Sharon L Guffy, Surya V S R K Pulavarti, Joseph Harrison, Drew Fleming, Thomas Szyperski, Brian Kuhlman
Inside-Out Design of Zinc-Binding Proteins with Non-Native Backbones. Biochemistry 62 (3) (2023)
Odessa J Goudy, Alice Peng, Ashutosh Tripathy, Brian Kuhlman
Design of a protease-activated PD-L1 inhibitor. Protein science : a publication of the Protein Society (2023)
Sharon L Guffy, Surya V S R K Pulavarti, Joseph Harrison, Drew Fleming, Thomas Szyperski, Brian Kuhlman
Inside-Out Design of Zinc-Binding Proteins with Non-Native Backbones. Biochemistry 62 (3) (2023)
Sharon L Guffy, Surya V S R K Pulavarti, Joseph Harrison, Drew Fleming, Thomas Szyperski, Brian Kuhlman
Inside-Out Design of Zinc-Binding Proteins with Non-Native Backbones. Biochemistry 62 (3) (2023)
Nicholas Z Randolph, Brian Kuhlman
Invariant point message passing for protein side chain packing. bioRxiv : the preprint server for biology (2023)
Matthew C Cummins, Ashutosh Tripathy, John Sondek, Brian Kuhlman
De novo design of stable proteins that efficaciously inhibit oncogenic G proteins. Protein science : a publication of the Protein Society (2023)
Nicholas Z Randolph, Brian Kuhlman
Invariant point message passing for protein side chain packing. bioRxiv : the preprint server for biology (2023)
Odessa J Goudy, Alice Peng, Ashutosh Tripathy, Brian Kuhlman
Design of a protease-activated PD-L1 inhibitor. Protein science : a publication of the Protein Society 32 (3) (2023)
Nicholas Z Randolph, Brian Kuhlman
Invariant point message passing for protein side chain packing. bioRxiv : the preprint server for biology (2023)
Odessa J Goudy, Amrita Nallathambi, Tomoaki Kinjo, Nicholas Z Randolph, Brian Kuhlman
In silico evolution of protein binders with deep learning models for structure prediction and sequence design. bioRxiv : the preprint server for biology (2023)
Nicholas Z Randolph, Brian Kuhlman
Invariant point message passing for protein side chain packing. bioRxiv : the preprint server for biology (2023)
Sharon L Guffy, Surya V S R K Pulavarti, Joseph Harrison, Drew Fleming, Thomas Szyperski, Brian Kuhlman
Inside-Out Design of Zinc-Binding Proteins with Non-Native Backbones. Biochemistry 62 (3) (2023)
Odessa J Goudy, Alice Peng, Ashutosh Tripathy, Brian Kuhlman
Design of a protease-activated PD-L1 inhibitor. Protein science : a publication of the Protein Society 32 (3) (2023)
Odessa J Goudy, Amrita Nallathambi, Tomoaki Kinjo, Nicholas Z Randolph, Brian Kuhlman
In silico evolution of autoinhibitory domains for a PD-L1 antagonist using deep learning models. Proceedings of the National Academy of Sciences of the United States of America 120 (49) (2023)
Sharon L Guffy, Surya V S R K Pulavarti, Joseph Harrison, Drew Fleming, Thomas Szyperski, Brian Kuhlman
Inside-Out Design of Zinc-Binding Proteins with Non-Native Backbones. Biochemistry 62 (3) (2023)
Henry Dieckhaus, Michael Brocidiacono, Nicholas Z Randolph, Brian Kuhlman
Transfer learning to leverage larger datasets for improved prediction of protein stability changes. bioRxiv : the preprint server for biology (2023)
Nicholas Z Randolph, Brian Kuhlman
Invariant point message passing for protein side chain packing. bioRxiv : the preprint server for biology (2023)
Sharon L Guffy, Surya V S R K Pulavarti, Joseph Harrison, Drew Fleming, Thomas Szyperski, Brian Kuhlman
Inside-Out Design of Zinc-Binding Proteins with Non-Native Backbones. Biochemistry (2023)
Rodney Park, Chayanid Ongpipattanakul, Satish K Nair, Albert A Bowers, Brian Kuhlman
Designer installation of a substrate recruitment domain to tailor enzyme specificity. Nature chemical biology (2022)
Rodney Park, Chayanid Ongpipattanakul, Satish K Nair, Albert A Bowers, Brian Kuhlman
Designer installation of a substrate recruitment domain to tailor enzyme specificity. Nature chemical biology (2022)
Matthew C Cummins, Tim M Jacobs, Frank D Teets, Frank DiMaio, Ashutosh Tripathy, Brian Kuhlman
AlphaFold accurately predicts distinct conformations based on the oligomeric state of a de novo designed protein. Protein science : a publication of the Protein Society 31 (7) (2022)
Surya V S R K Pulavarti, Jack B Maguire, Shirley Yuen, Joseph S Harrison, Jermel Griffin, Lakshmanane Premkumar, Edward A Esposito, George I Makhatadze, Angel E Garcia, Thomas M Weiss, Edward H Snell, Brian Kuhlman, Thomas Szyperski
From Protein Design to the Energy Landscape of a Cold Unfolding Protein. The journal of physical chemistry. B 126 (6) (2022)
Katherine I Albanese, Andrew Leaver-Fay, Joseph W Treacy, Rodney Park, Kendall N Houk, Brian Kuhlman, Marcey L Waters
Comparative Analysis of Sulfonium-π, Ammonium-π, and Sulfur-π Interactions and Relevance to SAM-Dependent Methyltransferases. Journal of the American Chemical Society 144 (6) (2022)
David F Thieker, Jack B Maguire, Stephan T Kudlacek, Andrew Leaver-Fay, Sergey Lyskov, Brian Kuhlman
Stabilizing proteins, simplified: A Rosetta-based webtool for predicting favorable mutations. Protein science : a publication of the Protein Society 31 (10) (2022)
Julia Koehler Leman, Sergey Lyskov, Steven M Lewis, Jared Adolf-Bryfogle, Rebecca F Alford, Kyle A Barlow, Ziv Ben-Aharon, Daniel P Farrell, Jason S Fell, William A Hansen, Ameya Harmalkar, Jeliazko R Jeliazkov, Georg Kuenze, Justyna Dorota Kryś, Ajasja Ljubetič, Amanda L Loshbaugh, Jack Maguire, Rocco Moretti, Vikram Khipple Mulligan, Morgan L Nance, Phuong T Nguyen, Shane Ó Conchúir, Shourya S Roy Burman, Rituparna Samanta, Shannon T Smith, Frank Teets, Johanna K S Tiemann, Andrew Watkins, Hope Woods, Brahm J Yachnin, Christopher D Bahl, Chris Bailey-Kellogg, Julien S Baker, Rachel J Hagey, Frank DiMaio, Sagar D Khare, Tanja Kortemme, Jason W Labonte, Kresten Lindorff-Larsen, Jens Meiler, William R Schief, Ora Schueler-Furman, Justin B Siegel, Amelie Stein, Vladimir Yarov-Yarovoy, Brian Kuhlman, Andrew Leaver-Fay, Dominik Gront, Jeffrey J Gray, Richard A Bonneau
Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature communications 12 (1) (2021)
Stephan T Kudlacek, Stefan W Metz, Devina Thiono, Alexander Matthew Payne, Thanh T N Phan, Shaomin Tian, Lawrence J Forsberg, Jack B Maguire, Ian Seim, Shu Zhang, Ashutosh Tripathy, Joseph S Harrison, Nathan I Nicely, Sandrine Soman, Michael K McCracken, Gregory D Gromowski, Richard G Jarman, Lakshmanane Premkumar, Arivianda M DeSilva, Brian Kuhlman
Designed, highly expressing, thermostable dengue virus 2 envelope protein dimers elicit quaternary epitope antibodies. Science advances 7 (42) (2021)
Julia Koehler Leman, Brian D Weitzner, Steven M Lewis, Jared Adolf-Bryfogle, Nawsad Alam, Rebecca F Alford, Melanie Aprahamian, Julien S Baker, Kyle A Barlow, Patrick Barth, Benjamin Basanta, Brian J Bender, Kristin Blacklock, Jaume Bonet, Scott E Boyken, Philip G Bradley, Chris Bystroff, Patrick Conway, Seth Cooper, Bruno E Correia, Brian Coventry, Rachel J Hagey, René M De Jong, Frank DiMaio, Lorna Dsilva, Roland L Dunbrack, Alexander S Ford, Brandon Frenz, Darwin Y Fu, Caleb Geniesse, Lukasz Goldschmidt, Ragul Gowthaman, Jeffrey J Gray, Dominik Gront, Sharon Guffy, Scott Horowitz, Po-Ssu Huang, Thomas Huber, Tim M Jacobs, Jeliazko R Jeliazkov, David K Johnson, Kalli Kappel, John Karanicolas, Hamed Khakzad, Karen R Khar, Sagar D Khare, Firas Khatib, Alisa Khramushin, Indigo C King, Robert Kleffner, Brian Koepnick, Tanja Kortemme, Georg Kuenze, Brian Kuhlman, Daisuke Kuroda, Jason W Labonte, Jason K Lai, Gideon Lapidoth, Andrew Leaver-Fay, Steffen Lindert, Thomas Linsky, Nir London, Joseph H Lubin, Sergey Lyskov, Jack Maguire, Lars Malmström, Enrique Marcos, Orly Marcu, Nicholas A Marze, Jens Meiler, Rocco Moretti, Vikram Khipple Mulligan, Santrupti Nerli, Christoffer Norn, Shane Ó'Conchúir, Noah Ollikainen, Sergey Ovchinnikov, Michael S Pacella, Xingjie Pan, Hahnbeom Park, Ryan E Pavlovicz, Manasi Pethe, Brian G Pierce, Kala Bharath Pilla, Barak Raveh, P Douglas Renfrew, Shourya S Roy Burman, Aliza Rubenstein, Marion F Sauer, Andreas Scheck, William R Schief, Ora Schueler-Furman, Yuval Sedan, Alexander M Sevy, Nikolaos G Sgourakis, Lei Shi, Justin B Siegel, Daniel-Adriano Silva, Shannon Smith, Yifan Song, Amelie Stein, Maria Szegedy, Frank D Teets, Summer B Thyme, Ray Yu-Ruei Wang, Andrew Watkins, Lior Zimmerman, Richard A Bonneau
Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature methods 17 (7) (2020)
Andrew M Lerner, Austin J Hepperla, Gregory R Keele, Hashem A Meriesh, Hayretin Yumerefendi, David Restrepo, Seth Zimmerman, James E Bear, Brian Kuhlman, Ian J Davis, Brian D Strahl
An optogenetic switch for the Set2 methyltransferase provides evidence for transcription-dependent and -independent dynamics of H3K36 methylation. Genome research 30 (11) (2020)
Jack B Maguire, Hugh K Haddox, Devin Strickland, Samer F Halabiya, Brian Coventry, Jermel R Griffin, Surya V S R K Pulavarti, Matthew Cummins, David F Thieker, Eric Klavins, Thomas Szyperski, Frank DiMaio, Julien S Baker, Brian Kuhlman
Perturbing the energy landscape for improved packing during computational protein design. Proteins 89 (4) (2020)
Karen Froning, Jack Maguire, Arlene Sereno, Flora Huang, Shawn Chang, Kenneth Weichert, Anton J Frommelt, Jessica Dong, Xiufeng Wu, Heather Austin, Elaine M Conner, Jonathan R Fitchett, Aik Roy Heng, Deepa Balasubramaniam, Mark T Hilgers, Brian Kuhlman, Stephen J Demarest
Computational stabilization of T cell receptors allows pairing with antibodies to form bispecifics. Nature communications 11 (1) (2020)
Sabine Studer, Douglas A Hansen, Zbigniew L Pianowski, Peer R E Mittl, Aaron Debon, Sharon L Guffy, Bryan S Der, Brian Kuhlman, Donald Hilvert
Evolution of a highly active and enantiospecific metalloenzyme from short peptides. Science (New York, N.Y.) 362 (6420) (2019)
Brian Kuhlman
Designing protein structures and complexes with the molecular modeling program Rosetta. The Journal of biological chemistry 294 (50) (2019)
Orrin J Stone, Neha Pankow, Bei Liu, Ved P Sharma, Robert J Eddy, Hui Wang, Andrew T Putz, Frank D Teets, Brian Kuhlman, John S Condeelis, Klaus M Hahn
Optogenetic control of cofilin and αTAT in living cells using Z-lock. Nature chemical biology 15 (12) (2019)
Brian Kuhlman, Philip G Bradley
Advances in protein structure prediction and design. Nature reviews. Molecular cell biology 20 (11) (2019)
Stephan T Kudlacek, Lakshmanane Premkumar, Stefan W Metz, Ashutosh Tripathy, Andrey A Bobkov, Alexander Matthew Payne, Stephen Graham, James A Brackbill, Michael J Miley, Aravinda M de Silva, Brian Kuhlman
Physiological temperatures reduce dimerization of dengue and Zika virus recombinant envelope proteins. The Journal of biological chemistry 293 (23) (2018)
Sharon L Guffy, Frank D Teets, Minnie I Langlois, Brian Kuhlman
Protocols for Requirement-Driven Protein Design in the Rosetta Modeling Program. Journal of chemical information and modeling 58 (5) (2018)
Andrew M Lerner, Hayretin Yumerefendi, Odessa J Goudy, Brian D Strahl, Brian Kuhlman
Engineering Improved Photoswitches for the Control of Nucleocytoplasmic Distribution. ACS synthetic biology 7 (12) (2018)
Mahmud Hussain, Steven P Angus, Brian Kuhlman
Engineering a Protein Binder Specific for p38α with Interface Expansion. Biochemistry 57 (30) (2018)
Jack B Maguire, Scott E Boyken, David Baker, Brian Kuhlman
Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design. Journal of chemical theory and computation 14 (5) (2018)
Hayretin Yumerefendi, Hui Wang, Daniel J Dickinson, Andrew M Lerner, Per Malkus, Bob Goldstein, Klaus Hahn, Brian Kuhlman
Light-Dependent Cytoplasmic Recruitment Enhances the Dynamic Range of a Nuclear Import Photoswitch. Chembiochem : a European journal of chemical biology 19 (12) (2018)