The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
Alford, Rebecca F, Leaver-Fay, Andrew, Jeliazkov, Jeliazko R, O’Meara, Matthew J, DiMaio, Frank P, Park, Hahnbeom, Shapovalov, Maxim V, Renfrew, P. Douglas, Mulligan, Vikram K, Kappel, Kalli, Labonte, Jason W, Pacella, Michael S, Bonneau, Richard, Bradley, Philip, Dunbrack, Roland L, Das, Rhiju, Baker, David, Kuhlman, Brian, Kortemme, Tanja, Gray, Jeffrey J
Published in Journal of chemical theory and computation (13.06.2017)
Published in Journal of chemical theory and computation (13.06.2017)
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Journal Article
Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein–Ligand Docking
Park, Hahnbeom, Zhou, Guangfeng, Baek, Minkyung, Baker, David, DiMaio, Frank
Published in Journal of chemical theory and computation (09.03.2021)
Published in Journal of chemical theory and computation (09.03.2021)
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Journal Article
EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy
Barad, Benjamin A, Echols, Nathaniel, Wang, Ray Yu-Ruei, Cheng, Yifan, DiMaio, Frank, Adams, Paul D, Fraser, James S
Published in Nature methods (01.10.2015)
Published in Nature methods (01.10.2015)
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Journal Article
Protein structure prediction using Rosetta in CASP12
Ovchinnikov, Sergey, Park, Hahnbeom, Kim, David E., DiMaio, Frank, Baker, David
Published in Proteins, structure, function, and bioinformatics (01.03.2018)
Published in Proteins, structure, function, and bioinformatics (01.03.2018)
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Journal Article
Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules
Park, Hahnbeom, Bradley, Philip, Greisen, Per, Liu, Yuan, Mulligan, Vikram Khipple, Kim, David E, Baker, David, DiMaio, Frank
Published in Journal of chemical theory and computation (13.12.2016)
Published in Journal of chemical theory and computation (13.12.2016)
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Journal Article
Relaxation of backbone bond geometry improves protein energy landscape modeling
Conway, Patrick, Tyka, Michael D., DiMaio, Frank, Konerding, David E., Baker, David
Published in Protein science (01.01.2014)
Published in Protein science (01.01.2014)
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Journal Article
Improving de novo protein binder design with deep learning
Bennett, Nathaniel R, Coventry, Brian, Goreshnik, Inna, Huang, Buwei, Allen, Aza, Vafeados, Dionne, Peng, Ying Po, Dauparas, Justas, Baek, Minkyung, Stewart, Lance, DiMaio, Frank, De Munck, Steven, Savvides, Savvas N, Baker, David
Published in Nature communications (06.05.2023)
Published in Nature communications (06.05.2023)
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Journal Article
Cryo-electron microscopy structure of the lipid droplet-formation protein seipin
Sui, Xuewu, Arlt, Henning, Brock, Kelly P, Lai, Zon Weng, DiMaio, Frank, Marks, Debora S, Liao, Maofu, Farese, Jr, Robert V, Walther, Tobias C
Published in The Journal of cell biology (03.12.2018)
Published in The Journal of cell biology (03.12.2018)
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Journal Article
Protein homology model refinement by large-scale energy optimization
Park, Hahnbeom, Ovchinnikov, Sergey, Kim, David E., DiMaio, Frank, Baker, David
Published in Proceedings of the National Academy of Sciences - PNAS (20.03.2018)
Published in Proceedings of the National Academy of Sciences - PNAS (20.03.2018)
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Journal Article
Structural basis for the initiation of eukaryotic transcription-coupled DNA repair
Xu, Jun, Lahiri, Indrajit, Wang, Wei, Wier, Adam, Cianfrocco, Michael A, Chong, Jenny, Hare, Alissa A, Dervan, Peter B, DiMaio, Frank, Leschziner, Andres E, Wang, Dong
Published in Nature (London) (30.11.2017)
Published in Nature (London) (30.11.2017)
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Journal Article
Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta
Wang, Ray Yu-Ruei, Song, Yifan, Barad, Benjamin A, Cheng, Yifan, Fraser, James S, DiMaio, Frank
Published in eLife (26.09.2016)
Published in eLife (26.09.2016)
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Journal Article
Automatic and accurate ligand structure determination guided by cryo-electron microscopy maps
Muenks, Andrew, Zepeda, Samantha, Zhou, Guangfeng, Veesler, David, DiMaio, Frank
Published in Nature communications (01.03.2023)
Published in Nature communications (01.03.2023)
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Journal Article
High thermodynamic stability of parametrically designed helical bundles
Huang, Po-Ssu, Oberdorfer, Gustav, Xu, Chunfu, Pei, Xue Y., Nannenga, Brent L., Rogers, Joseph M., DiMaio, Frank, Gonen, Tamir, Luisi, Ben, Baker, David
Published in Science (American Association for the Advancement of Science) (24.10.2014)
Published in Science (American Association for the Advancement of Science) (24.10.2014)
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Journal Article
Structure of the Type VI Secretion System Contractile Sheath
Kudryashev, Mikhail, Wang, Ray Yu-Ruei, Brackmann, Maximilian, Scherer, Sebastian, Maier, Timm, Baker, David, DiMaio, Frank, Stahlberg, Henning, Egelman, Edward H., Basler, Marek
Published in Cell (26.02.2015)
Published in Cell (26.02.2015)
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Journal Article
A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms
Mashtalir, Nazar, Suzuki, Hiroshi, Farrell, Daniel P., Sankar, Akshay, Luo, Jie, Filipovski, Martin, D’Avino, Andrew R., St. Pierre, Roodolph, Valencia, Alfredo M., Onikubo, Takashi, Roeder, Robert G., Han, Yan, He, Yuan, Ranish, Jeffrey A., DiMaio, Frank, Walz, Thomas, Kadoch, Cigall
Published in Cell (29.10.2020)
Published in Cell (29.10.2020)
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Journal Article