DiMaio, Frank

Accurate prediction of protein structures and interactions using a 3-track network

Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 5,549

Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models

Watson, J. L., Juergens, D., Bennett, N. R., Trippe, B. L., Yim, J., Eisenach, H. E., Ahern, W., Borst, A. J., Ragotte, R. J., Milles, L. F., et al. (2022) · Nature

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 2,369

De novo design of protein structure and function with RFdiffusion

Watson, J. L., Juergens, D., Bennett, N. R., Trippe, B. L., Yim, J., Eisenach, H. E., Ahern, W., Borst, A. J., Ragotte, R. J., Milles, L. F., et al. (2023) · Nature

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 2,325

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

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

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

EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

Barad, B. A., Echols, N., Wang, R. Y.-R., Cheng, Y., DiMaio, F., Adams, P. D., & Fraser, J. S. (2015) · Nature Methods

Advanced Electron Microscopy Techniques and ApplicationsEnzyme Structure and Function

Cited by 886

Crystal structure of a monomeric retroviral protease solved by protein folding game players

Foldit Contenders Group, Khatib, F., Foldit Void Crushers Group, DiMaio, F., Cooper, S., Kazmierczyk, M., Gilski, M., Krzywda, S., Zabranska, H., Pichova, I., et al. (2011) · Nature Structural & Molecular Biology

Enzyme Structure and FunctionProtein Structure and Dynamics

Cited by 540

Scaffolding protein functional sites using deep learning

Wang, J., Lisanza, S., Juergens, D., Tischer, D., Watson, J. L., Castro, K. M., Ragotte, R., Saragovi, A., Milles, L. F., Baek, M., et al. (2022) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 487

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

Wang, R. Y.-R., Song, Y., Barad, B. A., Cheng, Y., Fraser, J. S., & DiMaio, F. (2016) · eLife

Advanced Electron Microscopy Techniques and ApplicationsProtein Structure and Dynamics

Cited by 457

Near-atomic model of microtubule-tau interactions

Kellogg, E. H., Hejab, N. M. A., Poepsel, S., Downing, K. H., DiMaio, F., & Nogales, E. (2018) · Science

Alzheimer's disease research and treatmentsMicrotubule and mitosis dynamics

Cited by 416

Improving de novo protein binder design with deep learning

Bennett, N. R., Coventry, B., Goreshnik, I., Huang, B., Allen, A., Vafeados, D., Peng, Y. P., Dauparas, J., Baek, M., Stewart, L., et al. (2023) · Nature Communications

Protein Structure and Dynamicsvaccines and immunoinformatics approaches

Cited by 402

Accurate prediction of protein–nucleic acid complexes using RoseTTAFoldNA

Baek, M., McHugh, R., Anishchenko, I., Jiang, H., Baker, D., & DiMaio, F. (2024) · Nature Methods

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 372

Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta

DiMaio, F., Tyka, M. D., Baker, M. L., Chiu, W., & Baker, D. (2009) · Journal of Molecular Biology

Advanced Electron Microscopy Techniques and ApplicationsProtein Structure and Dynamics

Cited by 295

High thermodynamic stability of parametrically designed helical bundles

Huang, P.-S., Oberdorfer, G., Xu, C., Pei, X. Y., Nannenga, B. L., Rogers, J. M., DiMaio, F., Gonen, T., Luisi, B., & Baker, D. (2014) · Science

Protein Structure and DynamicsChemical Synthesis and Analysis

Cited by 277

Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors

Park, Y.-J., Walls, A. C., Wang, Z., Sauer, M. M., Li, W., Tortorici, M. A., Bosch, B.-J., DiMaio, F., & Veesler, D. (2019) · Nature Structural & Molecular Biology

SARS-CoV-2 and COVID-19 ResearchGlycosylation and Glycoproteins Research

Cited by 260

An artificial intelligence accelerated virtual screening platform for drug discovery

Zhou, G., Rusnac, D.-V., Park, H., Canzani, D., Nguyen, H. M., Stewart, L., Bush, M. F., Nguyen, P. T., Wulff, H., Yarov-Yarovoy, V., et al. (2024) · Nature Communications

Computational Drug Discovery Methodsvaccines and immunoinformatics approaches

Cited by 260

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

Cryo-EM Structure of Caspase-8 Tandem DED Filament Reveals Assembly and Regulation Mechanisms of the Death-Inducing Signaling Complex

Fu, T.-M., Li, Y., Lu, A., Li, Z., Vajjhala, P. R., Cruz, A. C., Srivastava, D. B., DiMaio, F., Penczek, P. A., Siegel, R. M., et al. (2016) · Molecular Cell

Cell death mechanisms and regulationInflammasome and immune disorders

Cited by 196

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

Structural and functional insight into regulation of kinesin-1 by microtubule-associated protein MAP7

Ferro, L. S., Fang, Q., Eshun-Wilson, L., Fernandes, J., Jack, A., Farrell, D. P., Golcuk, M., Huijben, T., Costa, K., Gur, M., et al. (2022) · Science

Microtubule and mitosis dynamicsGenetic and Kidney Cyst Diseases

Cited by 112

Seipin forms a flexible cage at lipid droplet formation sites

Arlt, H., Sui, X., Folger, B., Adams, C., Chen, X., Remme, R., Hamprecht, F. A., DiMaio, F., Liao, M., Goodman, J. M., et al. (2022) · Nature Structural & Molecular Biology

Lipid metabolism and biosynthesisProtein Structure and Dynamics

Cited by 107

Seipin forms a flexible cage at lipid droplet formation sites

Arlt, H., Sui, X., Folger, B., Adams, C., Chen, X., Remme, R., Hamprecht, F. A., DiMaio, F., Liao, M., Goodman, J. M., et al. (2021) · Nature Structural & Molecular Biology

Lipid metabolism and biosynthesisProtein Structure and Dynamics

Cited by 107