Kuhlman, Brian

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

Alford, R. F., Leaver-Fay, A., Jeliazkov, J. R., O’Meara, M. J., DiMaio, F. P., Park, H., Shapovalov, M. V., Renfrew, P. D., Mulligan, V. K., Kappel, K., et al. (2017) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 1,532

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., et al. (2020) · Nature Methods

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 888

Advances in protein structure prediction and design

Kuhlman, B., & Bradley, P. (2019) · Nature Reviews Molecular Cell Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 806

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

Hayashi-Takagi, A., Yagishita, S., Nakamura, M., Shirai, F., Wu, Y. I., Loshbaugh, A. L., Kuhlman, B., Hahn, K. M., & Kasai, H. (2015) · Nature

Neuroscience and Neuropharmacology ResearchMemory and Neural Mechanisms

Cited by 624

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

Dieckhaus, H., Brocidiacono, M., Randolph, N. Z., & Kuhlman, B. (2024) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 205

Computational Design of a Single Amino Acid Sequence that Can Switch between Two Distinct Protein Folds

Ambroggio, X. I., & Kuhlman, B. (2006) · Journal of the American Chemical Society

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 200

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

Van Nguyen, T., Lee, J. E., Sweredoski, M. J., Yang, S.-J., Jeon, S.-J., Harrison, J. S., Yim, J.-H., Lee, S. G., Handa, H., Kuhlman, B., et al. (2016) · Molecular Cell

Protein Degradation and InhibitorsUbiquitin and proteasome pathways

Cited by 177

Perturbing the energy landscape for improved packing during computational protein design

Maguire, J. B., Haddox, H. K., Strickland, D., Halabiya, S. F., Coventry, B., Griffin, J. R., Pulavarti, S. V. S. R. K., Cummins, M., Thieker, D. F., Klavins, E., et al. (2021) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 169

Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3

Kamadurai, H. B., Qiu, Y., Deng, A., Harrison, J. S., MacDonald, C., Actis, M., Rodrigues, P., Miller, D. J., Souphron, J., Lewis, S. M., et al. (2013) · eLife

Ubiquitin and proteasome pathwaysEnzyme Structure and Function

Cited by 165

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

Tsai, J., Bonneau, R., Morozov, A. V., Kuhlman, B., Rohl, C. A., & Baker, D. (2003) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 158

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

Cummins, M. C., Jacobs, T. M., Teets, F. D., DiMaio, F., Tripathy, A., & Kuhlman, B. (2022) · Protein Science

Protein Structure and DynamicsReceptor Mechanisms and Signaling

Cited by 15

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

Cummins, M. C., Jacobs, T. M., Teets, F. D., DiMaio, F., Tripathy, A., & Kuhlman, B. (2022) · Protein Science

Protein Structure and DynamicsReceptor Mechanisms and Signaling

Cited by 14

Invariant point message passing for protein side chain packing

Randolph, N. Z., & Kuhlman, B. (2023) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 10

Intensity Modulation of Trichromatic Split Fluorescent Proteins for Live Cell Mapping

Ishii, M., Kinjo, T., Kondo, Y., Terai, K., Aoki, K., Kuhlman, B., & Matsuda, M. (2025) · Cell Reports Methods

Advanced Fluorescence Microscopy TechniquesBiochemical and Structural Characterization

Cited by 0