Modeling Disordered Regions in Proteins Using Rosetta

by Wang, Ray Yu-Ruei, Han, Yan, Krassovsky, Kristina, Sheffler, William, Tyka, Michael, Baker, David
Published 2011

One contact for every twelve residues allows robust and accurate topology-level protein structure modeling

by Kim, David E., DiMaio, Frank, Wang, Ray Yu-Ruei, Song, Yifan, Baker, David
Published 2013

Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11

by Ovchinnikov, Sergey, Park, Hahnbeom, Kim, David E., Liu, Yuan, Wang, Ray Yu-Ruei, Baker, David
Published in Proteins (2016)

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

by Wang, Ray Yu-Ruei, Song, Yifan, Barad, Benjamin A, Cheng, Yifan, Fraser, James S, DiMaio, Frank
Published in eLife (2016)

Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta

by Ovchinnikov, Sergey, Kim, David E., Wang, Ray Yu-Ruei, Liu, Yuan, DiMaio, Frank, Baker, David
Published in Proteins (2016)

Atomic structure of Hsp90:Cdc37:Cdk4 reveals Hsp90 regulates kinase via dramatic unfolding

by Verba, Kliment A., Wang, Ray Yu-Ruei, Arakawa, Akihiko, Liu, Yanxin, Shirouzu, Mikako, Yokoyama, Shigeyuki, Agard, David A.
Published in Science (2016)

High resolution comparative modeling with RosettaCM

by Song, Yifan, DiMaio, Frank, Wang, Ray Yu-Ruei, Kim, David, Miles, Chris, Brunette, TJ, Thompson, James, Baker, David
Published 2013

EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy

by Barad, Benjamin A, Echols, Nathaniel, Wang, Ray Yu-Ruei, Cheng, Yifan, DiMaio, Frank, Adams, Paul D, Fraser, James S
Published in Nat Methods (2015)

Structural Basis of Mitochondrial Receptor Binding and Constriction by DRP1

by Kalia, Raghav, Wang, Ray Yu-Ruei, Yusuf, Ali, Thomas, Paul V., Agard, David A., Shaw, Janet M., Frost, Adam
Published in Nature (2018)

De novo protein structure determination from near-atomic resolution cryo-EM maps

by Wang, Ray Yu-Ruei, Kudryashev, Mikhail, Li, Xueming, Egelman, Edward H., Basler, Marek, Cheng, Yifan, Baker, David, DiMaio, Frank
Published in Nat Methods (2015)

Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy

by Blok, Neil B., Tan, Dongyan, Wang, Ray Yu-Ruei, Penczek, Pawel A., Baker, David, DiMaio, Frank, Rapoport, Tom A., Walz, Thomas
Published in Proc Natl Acad Sci U S A (2015)

Structure of the Type VI secretion system contractile sheath

by 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 (2015)

Macromolecular modeling and design in Rosetta: recent methods and frameworks

by Koehler Leman, Julia, Weitzner, Brian D, Lewis, Steven M, Adolf-Bryfogle, Jared, Alam, Nawsad, Alford, Rebecca F, Aprahamian, Melanie, Baker, David, Barlow, Kyle A, Barth, Patrick, Basanta, Benjamin, Bender, Brian J, Blacklock, Kristin, Bonet, Jaume, Boyken, Scott, Bradley, Phil, Bystroff, Chris, Conway, Patrick, Cooper, Seth, Correia, Bruno E, Coventry, Brian, Das, Rhiju, De Jong, René M, DiMaio, Frank, Dsilva, Lorna, Dunbrack, Roland, Ford, Alex, Frenz, Brandon, Fu, Darwin Y, Geniesse, Caleb, Goldschmidt, Lukasz, Gowthaman, Ragul, Gray, Jeffrey J, Gront, Dominik, Guffy, Sharon, Horowitz, Scott, Huang, Po-Ssu, Huber, Thomas, Jacobs, Tim M, Jeliazkov, Jeliazko R, Johnson, David K, Kappel, Kalli, Karanicolas, John, Khakzad, Hamed, Khar, Karen R, Khare, Sagar D, Khatib, Firas, Khramushin, Alisa, King, Indigo C, Kleffner, Robert, Koepnick, Brian, Kortemme, Tanja, Kuenze, Georg, Kuhlman, Brian, Kuroda, Daisuke, Labonte, Jason W, Lai, Jason K, Lapidoth, Gideon, Leaver-Fay, Andrew, Lindert, Steffen, Linsky, Thomas, London, Nir, Lubin, Joseph H, Lyskov, Sergey, Maguire, Jack, Malmström, Lars, Marcos, Enrique, Marcu, Orly, Marze, Nicholas A, Meiler, Jens, Moretti, Rocco, Mulligan, Vikram Khipple, Nerli, Santrupti, Norn, Christoffer, Ó’Conchúir, Shane, Ollikainen, Noah, Ovchinnikov, Sergey, Pacella, Michael S, Pan, Xingjie, Park, Hahnbeom, Pavlovicz, Ryan E, Pethe, Manasi, Pierce, Brian G, Pilla, Kala Bharath, Raveh, Barak, Renfrew, P Douglas, Roy Burman, Shourya S, Rubenstein, Aliza, Sauer, Marion F, Scheck, Andreas, Schief, William, Schueler-Furman, Ora, Sedan, Yuval, Sevy, Alexander M, Sgourakis, Nikolaos G, Shi, Lei, Siegel, Justin, Silva, Daniel-Adriano, Smith, Shannon, Song, Yifan, Stein, Amelie, Szegedy, Maria, Teets, Frank D, Thyme, Summer B, Wang, Ray Yu-Ruei, Watkins, Andrew, Zimmerman, Lior, Bonneau, Richard
Published in Nat Methods (2020)