Bera, Asim K.

Robust deep learning–based protein sequence design using ProteinMPNN

Dauparas, J., Anishchenko, I., Bennett, N., Bai, H., Ragotte, R. J., Milles, L. F., Wicky, B. I. M., Courbet, A., de Haas, R. J., Bethel, N., et al. (2022) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 2,210

Robust deep learning based protein sequence design using ProteinMPNN

Dauparas, J., Anishchenko, I., Bennett, N., Bai, H., Ragotte, R. J., Milles, L. F., Wicky, B. I. M., Courbet, A., de Haas, R. J., Bethel, N., et al. (2022) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 2,107

Generalized biomolecular modeling and design with RoseTTAFold All-Atom

Krishna, R., Wang, J., Ahern, W., Sturmfels, P., Venkatesh, P., Kalvet, I., Lee, G. R., Morey-Burrows, F. S., Anishchenko, I., Humphreys, I. R., et al. (2024) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 978

Design of protein-binding proteins from the target structure alone

Cao, L., Coventry, B., Goreshnik, I., Huang, B., Sheffler, W., Park, J. S., Jude, K. M., Marković, I., Kadam, R. U., Verschueren, K. H. G., et al. (2022) · Nature

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 577

Improving protein expression, stability, and function with ProteinMPNN

Sumida, K. H., Núñez-Franco, R., Kalvet, I., Pellock, S. J., Wicky, B. I. M., Milles, L. F., Dauparas, J., Wang, J., Kipnis, Y., Jameson, N., et al. (2023) · Journal of the American Chemical Society

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 344

Hallucinating symmetric protein assemblies

Wicky, B. I. M., Milles, L. F., Courbet, A., Ragotte, R. J., Dauparas, J., Kinfu, E., Tipps, S., Kibler, R. D., Baek, M., DiMaio, F., et al. (2022) · Science

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 240

Hallucinating protein assemblies

Wicky, B. I. M., Milles, L. F., Courbet, A., Ragotte, R. J., Dauparas, J., Kinfu, E., Tipps, S., Kibler, R. D., Baek, M., DiMaio, F., et al. (2022) · Science

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 240

Computational design of serine hydrolases

Lauko, A., Pellock, S. J., Sumida, K. H., Anishchenko, I., Juergens, D., Ahern, W., Jeung, J., Shida, A. F., Hunt, A., Kalvet, I., et al. (2025) · Science

Protein Structure and DynamicsEnzyme Catalysis and Immobilization

Cited by 235

Tissue-Specific Oncogenic Activity of KRASA146T

Poulin, E. J., Bera, A. K., Lu, J., Lin, Y.-J., Strasser, S. D., Paulo, J. A., Huang, T. Q., Morales, C., Yan, W., Cook, J., et al. (2019) · Cancer Discovery

Protein Kinase Regulation and GTPase SignalingProtein Tyrosine Phosphatases

Cited by 197

Design of stimulus-responsive two-state hinge proteins

Praetorius, F., Leung, P. J. Y., Tessmer, M. H., Broerman, A., Demakis, C., Dishman, A. F., Pillai, A., Idris, A., Juergens, D., Dauparas, J., et al. (2023) · Science

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 90

Design of stimulus-responsive two-state hinge proteins

Praetorius, F., Leung, P. J. Y., Tessmer, M. H., Broerman, A., Demakis, C., Dishman, A. F., Pillai, A., Idris, A., Juergens, D., Dauparas, J., et al. (2023) · Science

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 90

Diffusing protein binders to intrinsically disordered proteins

Liu, C., Wu, K., Choi, H., Han, H. L., Zhang, X., Watson, J. L., Ahn, G., Zhang, J. Z., Shijo, S., Good, L. L., et al. (2025) · Nature

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 79

KRASQ61H Preferentially Signals through MAPK in a RAF Dimer-Dependent Manner in Non–Small Cell Lung Cancer

Zhou, Z.-W., Ambrogio, C., Bera, A. K., Li, Q., Li, X.-X., Li, L., Son, J., Gondi, S., Li, J., Campbell, E., et al. (2020) · Cancer Research

Protein Kinase Regulation and GTPase SignalingMelanoma and MAPK Pathways

Cited by 60

Design of amyloidogenic peptide traps

Sahtoe, D. D., Andrzejewska, E. A., Han, H. L., Rennella, E., Schneider, M. M., Meisl, G., Ahlrichs, M., Decarreau, J., Nguyen, H., Kang, A., et al. (2024) · Nature Chemical Biology

Alzheimer's disease research and treatmentsProtein Structure and Dynamics

Cited by 48

Design of amyloidogenic peptide traps

Sahtoe, D. D., Andrzejewska, E. A., Han, H. L., Rennella, E., Schneider, M. M., Meisl, G., Ahlrichs, M., Decarreau, J., Nguyen, H., Kang, A., et al. (2023) · Nature Chemical Biology

Alzheimer's disease research and treatmentsProtein Structure and Dynamics

Cited by 48

Rapid and automated design of two-component protein nanomaterials using ProteinMPNN

de Haas, R. J., Brunette, N., Goodson, A., Dauparas, J., Yi, S. Y., Yang, E. C., Dowling, Q., Nguyen, H., Kang, A., Bera, A. K., et al. (2024) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 42

Rapid and automated design of two-component protein nanomaterials using ProteinMPNN

de Haas, R. J., Brunette, N., Goodson, A., Dauparas, J., Yi, S. Y., Yang, E. C., Dowling, Q., Nguyen, H., Kang, A., Bera, A. K., et al. (2023) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 42

Small-molecule binding and sensing with a designed protein family

Lee, G. R., Pellock, S. J., Norn, C., Tischer, D., Dauparas, J., Anischenko, I., Mercer, J. A. M., Kang, A., Bera, A., Nguyen, H., et al. (2023) · Nature Communications

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 41

Structure and Characterization of a Covalent Inhibitor of Src Kinase

Gurbani, D., Du, G., Henning, N. J., Rao, S., Bera, A. K., Zhang, T., Gray, N. S., & Westover, K. D. (2020) · Frontiers in Molecular Biosciences

Protein Kinase Regulation and GTPase SignalingCancer Mechanisms and Therapy

Cited by 29

Diffusing protein binders to intrinsically disordered proteins

Liu, C., Wu, K., Choi, H., Han, H., Zhang, X., Watson, J. L., Shijo, S., Bera, A. K., Kang, A., Brackenbrough, E., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 24

Parametrically guided design of beta barrels and transmembrane nanopores using deep learning

Kim, D. E., Watson, J. L., Juergens, D., Majumder, S., Sonigra, R., Gerben, S. R., Kang, A., Bera, A. K., Li, X., & Baker, D. (2024) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsNanopore and Nanochannel Transport Studies

Cited by 21

Parametrically guided design of beta barrels and transmembrane nanopores using deep learning

Kim, D. E., Watson, J. L., Juergens, D., Majumder, S., Sonigra, R., Gerben, S. R., Kang, A., Bera, A. K., Li, X., & Baker, D. (2025) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsNanopore and Nanochannel Transport Studies

Cited by 21

Computational design of serine hydrolases

Lauko, A., Pellock, S. J., Anischanka, I., Sumida, K. H., Juergens, D., Ahern, W., Shida, A., Hunt, A., Kalvet, I., Norn, C., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsEnzyme Catalysis and Immobilization

Cited by 16

Hallucination of closed repeat proteins containing central pockets

An, L., Hicks, D. R., Zorine, D., Dauparas, J., Wicky, B. I. M., Milles, L. F., Courbet, A., Bera, A. K., Nguyen, H., Kang, A., et al. (2023) · Nature Structural & Molecular Biology

Protein Structure and DynamicsBiochemical and Structural Characterization

Cited by 15