Modeling Disordered Regions in Proteins Using Rosetta

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

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

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

Structure prediction using sparse simulated NOE restraints with Rosetta in CASP11

por Ovchinnikov, Sergey, Park, Hahnbeom, Kim, David E., Liu, Yuan, Wang, Ray Yu-Ruei, Baker, David
Publicado en Proteins (2016)

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

por Wang, Ray Yu-Ruei, Song, Yifan, Barad, Benjamin A, Cheng, Yifan, Fraser, James S, DiMaio, Frank
Publicado en eLife (2016)

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

por Ovchinnikov, Sergey, Kim, David E., Wang, Ray Yu-Ruei, Liu, Yuan, DiMaio, Frank, Baker, David
Publicado en Proteins (2016)

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

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

High resolution comparative modeling with RosettaCM

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

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

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

Structural Basis of Mitochondrial Receptor Binding and Constriction by DRP1

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

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

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

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

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

Structure of the Type VI secretion system contractile sheath

por Kudryashev, Mikhail, Wang, Ray Yu-Ruei, Brackmann, Maximilian, Scherer, Sebastian, Maier, Timm, Baker, David, DiMaio, Frank, Stahlberg, Henning, Egelman, Edward H., Basler, Marek
Publicado en Cell (2015)

Macromolecular modeling and design in Rosetta: recent methods and frameworks

por 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
Publicado en Nat Methods (2020)