Watkins, Andrew M.

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

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OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization

Ahdritz, G., Bouatta, N., Floristean, C., Kadyan, S., Xia, Q., Gerecke, W., O’Donnell, T. J., Berenberg, D., Fisk, I., Zanichelli, N., et al. (2024) · Nature Methods

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 439

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

Leppek, K., Byeon, G. W., Kladwang, W., Wayment-Steele, H. K., Kerr, C. H., Xu, A. F., Kim, D. S., Topkar, V. V., Choe, C., Rothschild, D., et al. (2021) · Nature Communications

RNA and protein synthesis mechanismsRNA Interference and Gene Delivery

Cited by 399

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

Leppek, K., Byeon, G. W., Kladwang, W., Wayment-Steele, H. K., Kerr, C. H., Xu, A. F., Kim, D. S., Topkar, V. V., Choe, C., Rothschild, D., et al. (2022) · Nature Communications

RNA and protein synthesis mechanismsRNA Interference and Gene Delivery

Cited by 399

Theoretical basis for stabilizing messenger RNA through secondary structure design

Wayment-Steele, H. K., Kim, D. S., Choe, C. A., Nicol, J. J., Wellington-Oguri, R., Watkins, A. M., Sperberg, R. A. P., Huang, P.-S., Participants, E., & Das, R. (2020) · Nucleic Acids Research

RNA and protein synthesis mechanismsRNA Research and Splicing

Cited by 199

Theoretical basis for stabilizing messenger RNA through secondary structure design

Wayment-Steele, H. K., Kim, D. S., Choe, C. A., Nicol, J. J., Wellington-Oguri, R., Watkins, A. M., Parra Sperberg, R. A., Huang, P.-S., Participants, E., & Das, R. (2021) · Nucleic Acids Research

RNA and protein synthesis mechanismsRNA Research and Splicing

Cited by 197

Designing Peptides on a Quantum Computer

Mulligan, V. K., Melo, H., Merritt, H. I., Slocum, S., Weitzner, B. D., Watkins, A. M., Renfrew, P. D., Pelissier, C., Arora, P. S., & Bonneau, R. (2019) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsQuantum Computing Algorithms and Architecture

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Local structural flexibility drives oligomorphism in computationally designed protein assemblies

Khmelinskaia, A., Bethel, N. P., Fatehi, F., Antanasijevic, A., Borst, A. J., Lai, S.-H., Wang, J. Y. (., Mallik, B. B., Miranda, M. C., Watkins, A. M., et al. (2023) · Nature Structural & Molecular Biology

Protein Structure and DynamicsBiochemical and Structural Characterization

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Local structural flexibility drives oligomorphism in computationally designed protein assemblies

Khmelinskaia, A., Bethel, N. P., Fatehi, F., Mallik, B. B., Antanasijevic, A., Borst, A. J., Lai, S.-H., Chim, H. Y., Wang, J. Y. ‘., Miranda, M. C., et al. (2025) · Nature Structural & Molecular Biology

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 18