DiMaio Lab

Institute for Protein Design
University of Washington

Publications

2023

Roy, Anindya; Shi, Lei; Chang, Ashley; Dong, Xianchi; Fernandez, Andres; Kraft, John C; Li, Jing; Le, Viet Q; Winegar, Rebecca Viazzo; Cherf, Gerald Maxwell; Slocum, Dean; Poulson, P Daniel; Casper, Garrett E; Vallecillo-Zúniga, Mary L; Valdoz, Jonard Corpuz; Miranda, Marcos C; Bai, Hua; Kipnis, Yakov; Olshefsky, Audrey; Priya, Tanu; Carter, Lauren; Ravichandran, Rashmi; Chow, Cameron M; Johnson, Max R; Cheng, Suna; Smith, McKaela; Overed-Sayer, Catherine; Finch, Donna K; Lowe, David; Bera, Asim K; Matute-Bello, Gustavo; Birkland, Timothy P; DiMaio, Frank; Raghu, Ganesh; Cochran, Jennifer R; Stewart, Lance J; Campbell, Melody G; Ry, Pam M Van; Springer, Timothy; Baker, David

De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8 Journal Article

In: Nat Commun, vol. 14, no. 1, pp. 5660, 2023, ISSN: 2041-1723.

Abstract | Links | BibTeX

Watson, Joseph L; Juergens, David; Bennett, Nathaniel R; Trippe, Brian L; Yim, Jason; Eisenach, Helen E; Ahern, Woody; Borst, Andrew J; Ragotte, Robert J; Milles, Lukas F; Wicky, Basile I M; Hanikel, Nikita; Pellock, Samuel J; Courbet, Alexis; Sheffler, William; Wang, Jue; Venkatesh, Preetham; Sappington, Isaac; Torres, Susana Vázquez; Lauko, Anna; Bortoli, Valentin De; Mathieu, Emile; Ovchinnikov, Sergey; Barzilay, Regina; Jaakkola, Tommi S; DiMaio, Frank; Baek, Minkyung; Baker, David

De novo design of protein structure and function with RFdiffusion Journal Article

In: Nature, vol. 620, no. 7976, pp. 1089–1100, 2023, ISSN: 1476-4687.

Abstract | Links | BibTeX

Zhang, Min; Jungblut, Anna; Kunert, Franziska; Hauptmann, Luis; Hoffmann, Thomas; Kolesnikova, Olga; Metzner, Felix; Moldt, Manuela; Weis, Felix; DiMaio, Frank; Hopfner, Karl-Peter; Eustermann, Sebastian

Hexasome-INO80 complex reveals structural basis of noncanonical nucleosome remodeling Journal Article

In: Science, vol. 381, no. 6655, pp. 313–319, 2023, ISSN: 1095-9203.

Abstract | Links | BibTeX

Reggiano, Gabriella; Lugmayr, Wolfgang; Farrell, Daniel; Marlovits, Thomas C; DiMaio, Frank

Residue-level error detection in cryoelectron microscopy models Journal Article

In: Structure, vol. 31, no. 7, pp. 860–869.e4, 2023, ISSN: 1878-4186.

Abstract | Links | BibTeX

Bennett, Nathaniel R; Coventry, Brian; Goreshnik, Inna; Huang, Buwei; Allen, Aza; Vafeados, Dionne; Peng, Ying Po; Dauparas, Justas; Baek, Minkyung; Stewart, Lance; DiMaio, Frank; Munck, Steven De; Savvides, Savvas N; Baker, David

Improving de novo protein binder design with deep learning Journal Article

In: Nat Commun, vol. 14, no. 1, pp. 2625, 2023, ISSN: 2041-1723.

Abstract | Links | BibTeX

Muenks, Andrew; Zepeda, Samantha; Zhou, Guangfeng; Veesler, David; DiMaio, Frank

Automatic and accurate ligand structure determination guided by cryo-electron microscopy maps Journal Article

In: Nat Commun, vol. 14, no. 1, pp. 1164, 2023, ISSN: 2041-1723.

Abstract | Links | BibTeX

Selvaraj, Muniyandi; Kokate, Shrikant B; Reggiano, Gabriella; Kogan, Konstantin; Kotila, Tommi; Kremneva, Elena; DiMaio, Frank; Lappalainen, Pekka; Huiskonen, Juha T

Structural basis underlying specific biochemical activities of non-muscle tropomyosin isoforms Journal Article

In: Cell Rep, vol. 42, no. 1, pp. 111900, 2023, ISSN: 2211-1247.

Abstract | Links | BibTeX

Lugmayr, Wolfgang; Kotov, Vadim; Goessweiner-Mohr, Nikolaus; Wald, Jiri; DiMaio, Frank; Marlovits, Thomas C

StarMap: a user-friendly workflow for Rosetta-driven molecular structure refinement Journal Article

In: Nat Protoc, vol. 18, no. 1, pp. 239–264, 2023, ISSN: 1750-2799.

Abstract | Links | BibTeX

2022

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; Li, X; Carter, L; Kang, A; Nguyen, H; Bera, A K; Baker, D

Hallucinating symmetric protein assemblies Journal Article

In: Science, vol. 378, no. 6615, pp. 56–61, 2022, ISSN: 1095-9203.

Abstract | Links | BibTeX

Wang, Jue; Lisanza, Sidney; Juergens, David; Tischer, Doug; Watson, Joseph L; Castro, Karla M; Ragotte, Robert; Saragovi, Amijai; Milles, Lukas F; Baek, Minkyung; Anishchenko, Ivan; Yang, Wei; Hicks, Derrick R; Expòsit, Marc; Schlichthaerle, Thomas; Chun, Jung-Ho; Dauparas, Justas; Bennett, Nathaniel; Wicky, Basile I M; Muenks, Andrew; DiMaio, Frank; Correia, Bruno; Ovchinnikov, Sergey; Baker, David

Scaffolding protein functional sites using deep learning Journal Article

In: Science, vol. 377, no. 6604, pp. 387–394, 2022, ISSN: 1095-9203.

Abstract | Links | BibTeX

Cummins, Matthew C; Jacobs, Tim M; Teets, Frank D; DiMaio, Frank; Tripathy, Ashutosh; Kuhlman, Brian

AlphaFold accurately predicts distinct conformations based on the oligomeric state of a de novo designed protein Journal Article

In: Protein Sci, vol. 31, no. 7, pp. e4368, 2022, ISSN: 1469-896X.

Abstract | Links | BibTeX

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

Correction to “The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design” Miscellaneous

2022, ISSN: 1549-9626.

Links | BibTeX

Wang, Zhaoqian; Amaya, Moushimi; Addetia, Amin; Dang, Ha V; Reggiano, Gabriella; Yan, Lianying; Hickey, Andrew C; DiMaio, Frank; Broder, Christopher C; Veesler, David

Architecture and antigenicity of the Nipah virus attachment glycoprotein Journal Article

In: Science, vol. 375, no. 6587, pp. 1373–1378, 2022, ISSN: 1095-9203.

Abstract | Links | BibTeX

Arlt, Henning; Sui, Xuewu; Folger, Brayden; Adams, Carson; Chen, Xiao; Remme, Roman; Hamprecht, Fred A; DiMaio, Frank; Liao, Maofu; Goodman, Joel M; Farese, Robert V; Walther, Tobias C

Seipin forms a flexible cage at lipid droplet formation sites Journal Article

In: Nat Struct Mol Biol, vol. 29, no. 3, pp. 194–202, 2022, ISSN: 1545-9985.

Abstract | Links | BibTeX

Singer, Jedediah M; Novotney, Scott; Strickland, Devin; Haddox, Hugh K; Leiby, Nicholas; Rocklin, Gabriel J; Chow, Cameron M; Roy, Anindya; Bera, Asim K; Motta, Francis C; Cao, Longxing; Strauch, Eva-Maria; Chidyausiku, Tamuka M; Ford, Alex; Ho, Ethan; Zaitzeff, Alexander; Mackenzie, Craig O; Eramian, Hamed; DiMaio, Frank; Grigoryan, Gevorg; Vaughn, Matthew; Stewart, Lance J; Baker, David; Klavins, Eric

Large-scale design and refinement of stable proteins using sequence-only models Journal Article

In: PLoS One, vol. 17, no. 3, pp. e0265020, 2022, ISSN: 1932-6203.

Abstract | Links | BibTeX

Ferro, Luke S; Fang, Qianglin; Eshun-Wilson, Lisa; Fernandes, Jonathan; Jack, Amanda; Farrell, Daniel P; Golcuk, Mert; Huijben, Teun; Costa, Katelyn; Gur, Mert; DiMaio, Frank; Nogales, Eva; Yildiz, Ahmet

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

In: Science, vol. 375, no. 6578, pp. 326–331, 2022, ISSN: 1095-9203.

Abstract | Links | BibTeX

2021

Lieberman, Nicole A P; Lin, Michelle J; Xie, Hong; Shrestha, Lasata; Nguyen, Tien; Huang, Meei-Li; Haynes, Austin M; Romeis, Emily; Wang, Qian-Qiu; Zhang, Rui-Li; Kou, Cai-Xia; Ciccarese, Giulia; Conte, Ivano Dal; Cusini, Marco; Drago, Francesco; Nakayama, Shu-Ichi; Lee, Kenichi; Ohnishi, Makoto; Konda, Kelika A; Vargas, Silver K; Eguiluz, Maria; Caceres, Carlos F; Klausner, Jeffrey D; Mitjà, Oriol; Rompalo, Anne; Mulcahy, Fiona; Hook, Edward W; Lukehart, Sheila A; Casto, Amanda M; Roychoudhury, Pavitra; DiMaio, Frank; Giacani, Lorenzo; Greninger, Alexander L

Treponema pallidum genome sequencing from six continents reveals variability in vaccine candidate genes and dominance of Nichols clade strains in Madagascar Journal Article

In: PLoS Negl Trop Dis, vol. 15, no. 12, pp. e0010063, 2021, ISSN: 1935-2735.

Abstract | Links | BibTeX

Anishchenko, Ivan; Pellock, Samuel J; Chidyausiku, Tamuka M; Ramelot, Theresa A; Ovchinnikov, Sergey; Hao, Jingzhou; Bafna, Khushboo; Norn, Christoffer; Kang, Alex; Bera, Asim K; DiMaio, Frank; Carter, Lauren; Chow, Cameron M; Montelione, Gaetano T; Baker, David

De novo protein design by deep network hallucination Journal Article

In: Nature, vol. 600, no. 7889, pp. 547–552, 2021, ISSN: 1476-4687.

Abstract | Links | BibTeX

Leman, Julia Koehler; Lyskov, Sergey; Lewis, Steven M; Adolf-Bryfogle, Jared; Alford, Rebecca F; Barlow, Kyle; Ben-Aharon, Ziv; Farrell, Daniel; Fell, Jason; Hansen, William A; Harmalkar, Ameya; Jeliazkov, Jeliazko; Kuenze, Georg; Krys, Justyna D; Ljubetič, Ajasja; Loshbaugh, Amanda L; Maguire, Jack; Moretti, Rocco; Mulligan, Vikram Khipple; Nance, Morgan L; Nguyen, Phuong T; Conchúir, Shane Ó; Burman, Shourya S Roy; Samanta, Rituparna; Smith, Shannon T; Teets, Frank; Tiemann, Johanna K S; Watkins, Andrew; Woods, Hope; Yachnin, Brahm J; Bahl, Christopher D; Bailey-Kellogg, Chris; Baker, David; Das, Rhiju; DiMaio, Frank; Khare, Sagar D; Kortemme, Tanja; Labonte, Jason W; Lindorff-Larsen, Kresten; Meiler, Jens; Schief, William; Schueler-Furman, Ora; Siegel, Justin B; Stein, Amelie; Yarov-Yarovoy, Vladimir; Kuhlman, Brian; Leaver-Fay, Andrew; Gront, Dominik; Gray, Jeffrey J; Bonneau, Richard

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks Journal Article

In: Nat Commun, vol. 12, no. 1, pp. 6947, 2021, ISSN: 2041-1723.

Abstract | Links | BibTeX

Hansen, Jesse M; Horowitz, Avital; Lynch, Eric M; Farrell, Daniel P; Quispe, Joel; DiMaio, Frank; Kollman, Justin M

Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation Journal Article

In: Elife, vol. 10, 2021, ISSN: 2050-084X.

Abstract | Links | BibTeX

Kacherovsky, Nataly; Yang, Lucy F; Dang, Ha V; Cheng, Emmeline L; Cardle, Ian I; Walls, Alexandra C; McCallum, Matthew; Sellers, Drew L; DiMaio, Frank; Salipante, Stephen J; Corti, Davide; Veesler, David; Pun, Suzie H

Discovery and Characterization of Spike N-Terminal Domain-Binding Aptamers for Rapid SARS-CoV-2 Detection Journal Article

In: Angew Chem Int Ed Engl, vol. 60, no. 39, pp. 21211–21215, 2021, ISSN: 1521-3773.

Abstract | Links | BibTeX

Rathinaswamy, Manoj K; Dalwadi, Udit; Fleming, Kaelin D; Adams, Carson; Stariha, Jordan T B; Pardon, Els; Baek, Minkyung; Vadas, Oscar; DiMaio, Frank; Steyaert, Jan; Hansen, Scott D; Yip, Calvin K; Burke, John E

Structure of the phosphoinositide 3-kinase (PI3K) p110γ-p101 complex reveals molecular mechanism of GPCR activation Journal Article

In: Sci Adv, vol. 7, no. 35, 2021, ISSN: 2375-2548.

Abstract | Links | BibTeX

Baek, Minkyung; DiMaio, Frank; Anishchenko, Ivan; Dauparas, Justas; Ovchinnikov, Sergey; Lee, Gyu Rie; Wang, Jue; Cong, Qian; Kinch, Lisa N; Schaeffer, R Dustin; Millán, Claudia; Park, Hahnbeom; Adams, Carson; Glassman, Caleb R; DeGiovanni, Andy; Pereira, Jose H; Rodrigues, Andria V; van Dijk, Alberdina A; Ebrecht, Ana C; Opperman, Diederik J; Sagmeister, Theo; Buhlheller, Christoph; Pavkov-Keller, Tea; Rathinaswamy, Manoj K; Dalwadi, Udit; Yip, Calvin K; Burke, John E; Garcia, K Christopher; Grishin, Nick V; Adams, Paul D; Read, Randy J; Baker, David

Accurate prediction of protein structures and interactions using a three-track neural network Journal Article

In: Science, vol. 373, no. 6557, pp. 871–876, 2021, ISSN: 1095-9203.

Abstract | Links | BibTeX

Wu, Jinming; Blum, Thorsten B; Farrell, Daniel P; DiMaio, Frank; Abrahams, Jan Pieter; Luo, Jinghui

Cryo-electron Microscopy Imaging of Alzheimer’s Amyloid-beta 42 Oligomer Displayed on a Functionally and Structurally Relevant Scaffold Journal Article

In: Angew Chem Int Ed Engl, vol. 60, no. 34, pp. 18680–18687, 2021, ISSN: 1521-3773.

Abstract | Links | BibTeX

Bryan, Cassie M; Rocklin, Gabriel J; Bick, Matthew J; Ford, Alex; Majri-Morrison, Sonia; Kroll, Ashley V; Miller, Chad J; Carter, Lauren; Goreshnik, Inna; Kang, Alex; DiMaio, Frank; Tarbell, Kristin V; Baker, David

Computational design of a synthetic PD-1 agonist Journal Article

In: Proc Natl Acad Sci U S A, vol. 118, no. 29, 2021, ISSN: 1091-6490.

Abstract | Links | BibTeX

Chi, Gamma; Ebenhoch, Rebecca; Man, Henry; Tang, Haiping; Tremblay, Laurence E; Reggiano, Gabriella; Qiu, Xingyu; Bohstedt, Tina; Liko, Idlir; Almeida, Fernando G; Garneau, Alexandre P; Wang, Dong; McKinley, Gavin; Moreau, Christophe P; Bountra, Kiran D; Abrusci, Patrizia; Mukhopadhyay, Shubhashish M M; Fernandez-Cid, Alejandra; Slimani, Samira; Lavoie, Julie L; Burgess-Brown, Nicola A; Tehan, Ben; DiMaio, Frank; Jazayeri, Ali; Isenring, Paul; Robinson, Carol V; Dürr, Katharina L

Phospho-regulation, nucleotide binding and ion access control in potassium-chloride cotransporters Journal Article

In: EMBO J, vol. 40, no. 14, pp. e107294, 2021, ISSN: 1460-2075.

Abstract | Links | BibTeX

Mann, Daniel; Fan, Junping; Somboon, Kamolrat; Farrell, Daniel P; Muenks, Andrew; Tzokov, Svetomir B; DiMaio, Frank; Khalid, Syma; Miller, Samuel I; Bergeron, Julien R C

Structure and lipid dynamics in the maintenance of lipid asymmetry inner membrane complex of A. baumannii Journal Article

In: Commun Biol, vol. 4, no. 1, pp. 817, 2021, ISSN: 2399-3642.

Abstract | Links | BibTeX

Dai, Gucan; Aman, Teresa K; DiMaio, Frank; Zagotta, William N

Electromechanical coupling mechanism for activation and inactivation of an HCN channel Journal Article

In: Nat Commun, vol. 12, no. 1, pp. 2802, 2021, ISSN: 2041-1723.

Abstract | Links | BibTeX

Maguire, Jack B; Haddox, Hugh K; Strickland, Devin; Halabiya, Samer F; Coventry, Brian; Griffin, Jermel R; Pulavarti, Surya V S R K; Cummins, Matthew; Thieker, David F; Klavins, Eric; Szyperski, Thomas; DiMaio, Frank; Baker, David; Kuhlman, Brian

Perturbing the energy landscape for improved packing during computational protein design Journal Article

In: Proteins, vol. 89, no. 4, pp. 436–449, 2021, ISSN: 1097-0134.

Abstract | Links | BibTeX

Witus, Samuel R; Burrell, Anika L; Farrell, Daniel P; Kang, Jianming; Wang, Meiling; Hansen, Jesse M; Pravat, Alex; Tuttle, Lisa M; Stewart, Mikaela D; Brzovic, Peter S; Chatterjee, Champak; Zhao, Weixing; DiMaio, Frank; Kollman, Justin M; Klevit, Rachel E

BRCA1/BARD1 site-specific ubiquitylation of nucleosomal H2A is directed by BARD1 Journal Article

In: Nat Struct Mol Biol, vol. 28, no. 3, pp. 268–277, 2021, ISSN: 1545-9985.

Abstract | Links | BibTeX

Park, Hahnbeom; Zhou, Guangfeng; Baek, Minkyung; Baker, David; DiMaio, Frank

Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein-Ligand Docking Journal Article

In: J Chem Theory Comput, vol. 17, no. 3, pp. 2000–2010, 2021, ISSN: 1549-9626.

Abstract | Links | BibTeX

Lawson, Catherine L; Kryshtafovych, Andriy; Adams, Paul D; Afonine, Pavel V; Baker, Matthew L; Barad, Benjamin A; Bond, Paul; Burnley, Tom; Cao, Renzhi; Cheng, Jianlin; Chojnowski, Grzegorz; Cowtan, Kevin; Dill, Ken A; DiMaio, Frank; Farrell, Daniel P; Fraser, James S; Herzik, Mark A; Hoh, Soon Wen; Hou, Jie; Hung, Li-Wei; Igaev, Maxim; Joseph, Agnel P; Kihara, Daisuke; Kumar, Dilip; Mittal, Sumit; Monastyrskyy, Bohdan; Olek, Mateusz; Palmer, Colin M; Patwardhan, Ardan; Perez, Alberto; Pfab, Jonas; Pintilie, Grigore D; Richardson, Jane S; Rosenthal, Peter B; Sarkar, Daipayan; Schäfer, Luisa U; Schmid, Michael F; Schröder, Gunnar F; Shekhar, Mrinal; Si, Dong; Singharoy, Abishek; Terashi, Genki; Terwilliger, Thomas C; Vaiana, Andrea; Wang, Liguo; Wang, Zhe; Wankowicz, Stephanie A; Williams, Christopher J; Winn, Martyn; Wu, Tianqi; Yu, Xiaodi; Zhang, Kaiming; Berman, Helen M; Chiu, Wah

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge Journal Article

In: Nat Methods, vol. 18, no. 2, pp. 156–164, 2021, ISSN: 1548-7105.

Abstract | Links | BibTeX

2020

Rule, Chelsea S; Park, Young-Jun; Delarosa, Jaclyn R; Turley, Stewart; Hol, Wim G J; McColm, Sarah; Gura, Colby; DiMaio, Frank; Korotkov, Konstantin V; Sandkvist, Maria

Suppressor Mutations in Type II Secretion Mutants of Vibrio cholerae: Inactivation of the VesC Protease Journal Article

In: mSphere, vol. 5, no. 6, 2020, ISSN: 2379-5042.

Abstract | Links | BibTeX

Zhang, Yue; Prach, Lisa M; O’Brien, Terrence E; DiMaio, Frank; Prigozhin, Daniil M; Corn, Jacob E; Alber, Tom; Siegel, Justin B; Tantillo, Dean J

Crystal Structure and Mechanistic Molecular Modeling Studies of Diterpene Cyclase Rv3377c Journal Article

In: Biochemistry, vol. 59, no. 47, pp. 4507–4515, 2020, ISSN: 1520-4995.

Abstract | Links | BibTeX

Mulligan, Vikram Khipple; Kang, Christine S; Sawaya, Michael R; Rettie, Stephen; Li, Xinting; Antselovich, Inna; Craven, Timothy W; Watkins, Andrew M; Labonte, Jason W; DiMaio, Frank; Yeates, Todd O; Baker, David

Computational design of mixed chirality peptide macrocycles with internal symmetry Journal Article

In: Protein Sci, vol. 29, no. 12, pp. 2433–2445, 2020, ISSN: 1469-896X.

Abstract | Links | BibTeX

Mashtalir, Nazar; Suzuki, Hiroshi; Farrell, Daniel P; Sankar, Akshay; Luo, Jie; Filipovski, Martin; D’Avino, Andrew R; Pierre, Roodolph St; Valencia, Alfredo M; Onikubo, Takashi; Roeder, Robert G; Han, Yan; He, Yuan; Ranish, Jeffrey A; DiMaio, Frank; Walz, Thomas; Kadoch, Cigall

A Structural Model of the Endogenous Human BAF Complex Informs Disease Mechanisms Journal Article

In: Cell, vol. 183, no. 3, pp. 802–817.e24, 2020, ISSN: 1097-4172.

Abstract | Links | BibTeX

Pavlovicz, Ryan E; Park, Hahnbeom; DiMaio, Frank

Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination Journal Article

In: PLoS Comput Biol, vol. 16, no. 9, pp. e1008103, 2020, ISSN: 1553-7358.

Abstract | Links | BibTeX

Farrell, Daniel P; Anishchenko, Ivan; Shakeel, Shabih; Lauko, Anna; Passmore, Lori A; Baker, David; DiMaio, Frank

Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM Journal Article

In: IUCrJ, vol. 7, no. Pt 5, pp. 881–892, 2020, ISSN: 2052-2525.

Abstract | Links | BibTeX

Xu, Chunfu; Lu, Peilong; El-Din, Tamer M Gamal; Pei, Xue Y; Johnson, Matthew C; Uyeda, Atsuko; Bick, Matthew J; Xu, Qi; Jiang, Daohua; Bai, Hua; Reggiano, Gabriella; Hsia, Yang; Brunette, T J; Dou, Jiayi; Ma, Dan; Lynch, Eric M; Boyken, Scott E; Huang, Po-Ssu; Stewart, Lance; DiMaio, Frank; Kollman, Justin M; Luisi, Ben F; Matsuura, Tomoaki; Catterall, William A; Baker, David

Computational design of transmembrane pores Journal Article

In: Nature, vol. 585, no. 7823, pp. 129–134, 2020, ISSN: 1476-4687.

Abstract | Links | BibTeX

Basanta, Benjamin; Bick, Matthew J; Bera, Asim K; Norn, Christoffer; Chow, Cameron M; Carter, Lauren P; Goreshnik, Inna; Dimaio, Frank; Baker, David

An enumerative algorithm for de novo design of proteins with diverse pocket structures Journal Article

In: Proc Natl Acad Sci U S A, vol. 117, no. 36, pp. 22135–22145, 2020, ISSN: 1091-6490.

Abstract | Links | BibTeX

Bhargava, Hersh K; Tabata, Keisuke; Byck, Jordan M; Hamasaki, Maho; Farrell, Daniel P; Anishchenko, Ivan; DiMaio, Frank; Im, Young Jun; Yoshimori, Tamotsu; Hurley, James H

Structural basis for autophagy inhibition by the human Rubicon-Rab7 complex Journal Article

In: Proc Natl Acad Sci U S A, vol. 117, no. 29, pp. 17003–17010, 2020, ISSN: 1091-6490.

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Leman, Julia Koehler; 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 E; Bradley, Phil; Bystroff, Chris; Conway, Patrick; Cooper, Seth; Correia, Bruno E; Coventry, Brian; Das, Rhiju; Jong, René M De; DiMaio, Frank; Dsilva, Lorna; Dunbrack, Roland; Ford, Alexander S; 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; Burman, Shourya S Roy; Rubenstein, Aliza; Sauer, Marion F; Scheck, Andreas; Schief, William; Schueler-Furman, Ora; Sedan, Yuval; Sevy, Alexander M; Sgourakis, Nikolaos G; Shi, Lei; Siegel, Justin B; 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

Macromolecular modeling and design in Rosetta: recent methods and frameworks Journal Article

In: Nat Methods, vol. 17, no. 7, pp. 665–680, 2020, ISSN: 1548-7105.

Abstract | Links | BibTeX

Al-Otaibi, Natalie S; Taylor, Aidan J; Farrell, Daniel P; Tzokov, Svetomir B; DiMaio, Frank; Kelly, David J; Bergeron, Julien R C

The cryo-EM structure of the bacterial flagellum cap complex suggests a molecular mechanism for filament elongation Journal Article

In: Nat Commun, vol. 11, no. 1, pp. 3210, 2020, ISSN: 2041-1723.

Abstract | Links | BibTeX

Evans, Eric G B; Morgan, Jacob L W; DiMaio, Frank; Zagotta, William N; Stoll, Stefan

Allosteric conformational change of a cyclic nucleotide-gated ion channel revealed by DEER spectroscopy Journal Article

In: Proc Natl Acad Sci U S A, vol. 117, no. 20, pp. 10839–10847, 2020, ISSN: 1091-6490.

Abstract | Links | BibTeX

Stoddard, Patrick R; Lynch, Eric M; Farrell, Daniel P; Dosey, Annie M; DiMaio, Frank; Williams, Tom A; Kollman, Justin M; Murray, Andrew W; Garner, Ethan C

Polymerization in the actin ATPase clan regulates hexokinase activity in yeast Journal Article

In: Science, vol. 367, no. 6481, pp. 1039–1042, 2020, ISSN: 1095-9203.

Abstract | Links | BibTeX

Frenz, Brandon; Lewis, Steven M; King, Indigo; DiMaio, Frank; Park, Hahnbeom; Song, Yifan

Prediction of Protein Mutational Free Energy: Benchmark and Sampling Improvements Increase Classification Accuracy Journal Article

In: Front Bioeng Biotechnol, vol. 8, pp. 558247, 2020, ISSN: 2296-4185.

Abstract | Links | BibTeX

2019

Park, Young-Jun; Walls, Alexandra C; Wang, Zhaoqian; Sauer, Maximillian M; Li, Wentao; Tortorici, M Alejandra; Bosch, Berend-Jan; DiMaio, Frank; Veesler, David

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

In: Nat Struct Mol Biol, vol. 26, no. 12, pp. 1151–1157, 2019, ISSN: 1545-9985.

Abstract | Links | BibTeX

Berman, Helen M; Adams, Paul D; Bonvin, Alexandre A; Burley, Stephen K; Carragher, Bridget; Chiu, Wah; DiMaio, Frank; Ferrin, Thomas E; Gabanyi, Margaret J; Goddard, Thomas D; Griffin, Patrick R; Haas, Juergen; Hanke, Christian A; Hoch, Jeffrey C; Hummer, Gerhard; Kurisu, Genji; Lawson, Catherine L; Leitner, Alexander; Markley, John L; Meiler, Jens; Montelione, Gaetano T; Phillips, George N; Prisner, Thomas; Rappsilber, Juri; Schriemer, David C; Schwede, Torsten; Seidel, Claus A M; Strutzenberg, Timothy S; Svergun, Dmitri I; Tajkhorshid, Emad; Trewhella, Jill; Vallat, Brinda; Velankar, Sameer; Vuister, Geerten W; Webb, Benjamin; Westbrook, John D; White, Kate L; Sali, Andrej

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures Miscellaneous

2019, ISSN: 1878-4186.

Abstract | Links | BibTeX

Park, Jung-Eun; Zhang, Liang; Bang, Jeong Kyu; Andresson, Thorkell; DiMaio, Frank; Lee, Kyung S

Phase separation of Polo-like kinase 4 by autoactivation and clustering drives centriole biogenesis Journal Article

In: Nat Commun, vol. 10, no. 1, pp. 4959, 2019, ISSN: 2041-1723.

Abstract | Links | BibTeX

Chou, Hui-Ting; Apelt, Luise; Farrell, Daniel P; White, Susan Roehl; Woodsmith, Jonathan; Svetlov, Vladimir; Goldstein, Jaclyn S; Nager, Andrew R; Li, Zixuan; Muller, Jean; Dollfus, Hélène; Nudler, Evgeny; Stelzl, Ulrich; DiMaio, Frank; Nachury, Maxence V; Walz, Thomas

The Molecular Architecture of Native BBSome Obtained by an Integrated Structural Approach Journal Article

In: Structure, vol. 27, no. 9, pp. 1384–1394.e4, 2019, ISSN: 1878-4186.

Abstract | Links | BibTeX

Lahiri, Indrajit; Xu, Jun; Han, Bong Gyoon; Oh, Juntaek; Wang, Dong; DiMaio, Frank; Leschziner, Andres E

3.1 Å structure of yeast RNA polymerase II elongation complex stalled at a cyclobutane pyrimidine dimer lesion solved using streptavidin affinity grids Journal Article

In: J Struct Biol, vol. 207, no. 3, pp. 270–278, 2019, ISSN: 1095-8657.

Abstract | Links | BibTeX

Dai, Gucan; Aman, Teresa K; DiMaio, Frank; Zagotta, William N

The HCN channel voltage sensor undergoes a large downward motion during hyperpolarization Journal Article

In: Nat Struct Mol Biol, vol. 26, no. 8, pp. 686–694, 2019, ISSN: 1545-9985.

Abstract | Links | BibTeX

Wang, Fengbin; Cvirkaite-Krupovic, Virginija; Kreutzberger, Mark A B; Su, Zhangli; de Oliveira, Guilherme A P; Osinski, Tomasz; Sherman, Nicholas; DiMaio, Frank; Wall, Joseph S; Prangishvili, David; Krupovic, Mart; Egelman, Edward H

An extensively glycosylated archaeal pilus survives extreme conditions Journal Article

In: Nat Microbiol, vol. 4, no. 8, pp. 1401–1410, 2019, ISSN: 2058-5276.

Abstract | Links | BibTeX

Kang, Shoukai; Davidsen, Kristian; Gomez-Castillo, Luis; Jiang, Huayi; Fu, Xiaonan; Li, Zengpeng; Liang, Yu; Jahn, Molly; Moussa, Mahmoud; DiMaio, Frank; Gu, Liangcai

COMBINES-CID: An Efficient Method for De Novo Engineering of Highly Specific Chemically Induced Protein Dimerization Systems Journal Article

In: J Am Chem Soc, vol. 141, no. 28, pp. 10948–10952, 2019, ISSN: 1520-5126.

Abstract | Links | BibTeX

Koepnick, Brian; Flatten, Jeff; Husain, Tamir; Ford, Alex; Silva, Daniel-Adriano; Bick, Matthew J; Bauer, Aaron; Liu, Gaohua; Ishida, Yojiro; Boykov, Alexander; Estep, Roger D; Kleinfelter, Susan; Nørgård-Solano, Toke; Wei, Linda; Players, Foldit; Montelione, Gaetano T; DiMaio, Frank; Popović, Zoran; Khatib, Firas; Cooper, Seth; Baker, David

De novo protein design by citizen scientists Journal Article

In: Nature, vol. 570, no. 7761, pp. 390–394, 2019, ISSN: 1476-4687.

Abstract | Links | BibTeX

Rizo, Alexandrea N; Lin, JiaBei; Gates, Stephanie N; Tse, Eric; Bart, Stephen M; Castellano, Laura M; DiMaio, Frank; Shorter, James; Southworth, Daniel R

Structural basis for substrate gripping and translocation by the ClpB AAA+ disaggregase Journal Article

In: Nat Commun, vol. 10, no. 1, pp. 2393, 2019, ISSN: 2041-1723.

Abstract | Links | BibTeX

Ilca, Serban L; Sun, Xiaoyu; Omari, Kamel El; Kotecha, Abhay; de Haas, Felix; DiMaio, Frank; Grimes, Jonathan M; Stuart, David I; Poranen, Minna M; Huiskonen, Juha T

Multiple liquid crystalline geometries of highly compacted nucleic acid in a dsRNA virus Journal Article

In: Nature, vol. 570, no. 7760, pp. 252–256, 2019, ISSN: 1476-4687.

Abstract | Links | BibTeX

Chen, Zibo; Johnson, Matthew C; Chen, Jiajun; Bick, Matthew J; Boyken, Scott E; Lin, Baihan; Yoreo, James J De; Kollman, Justin M; Baker, David; DiMaio, Frank

Self-Assembling 2D Arrays with de Novo Protein Building Blocks Journal Article

In: J Am Chem Soc, vol. 141, no. 22, pp. 8891–8895, 2019, ISSN: 1520-5126.

Abstract | Links | BibTeX

Chen, Zibo; Boyken, Scott E; Jia, Mengxuan; Busch, Florian; Flores-Solis, David; Bick, Matthew J; Lu, Peilong; VanAernum, Zachary L; Sahasrabuddhe, Aniruddha; Langan, Robert A; Bermeo, Sherry; Brunette, T J; Mulligan, Vikram Khipple; Carter, Lauren P; DiMaio, Frank; Sgourakis, Nikolaos G; Wysocki, Vicki H; Baker, David

Programmable design of orthogonal protein heterodimers Journal Article

In: Nature, vol. 565, no. 7737, pp. 106–111, 2019, ISSN: 1476-4687.

Abstract | Links | BibTeX

Frenz, Brandon; Rämisch, Sebastian; Borst, Andrew J; Walls, Alexandra C; Adolf-Bryfogle, Jared; Schief, William R; Veesler, David; DiMaio, Frank

Automatically Fixing Errors in Glycoprotein Structures with Rosetta Journal Article

In: Structure, vol. 27, no. 1, pp. 134–139.e3, 2019, ISSN: 1878-4186.

Abstract | Links | BibTeX

2018

Park, Young-Jun; Lacourse, Kaitlyn D; Cambillau, Christian; DiMaio, Frank; Mougous, Joseph D; Veesler, David

Structure of the type VI secretion system TssK-TssF-TssG baseplate subcomplex revealed by cryo-electron microscopy Journal Article

In: Nat Commun, vol. 9, no. 1, pp. 5385, 2018, ISSN: 2041-1723.

Abstract | Links | BibTeX

Sui, Xuewu; Arlt, Henning; Brock, Kelly P; Lai, Zon Weng; DiMaio, Frank; Marks, Debora S; Liao, Maofu; Farese, Robert V; Walther, Tobias C

Cryo-electron microscopy structure of the lipid droplet-formation protein seipin Journal Article

In: J Cell Biol, vol. 217, no. 12, pp. 4080–4091, 2018, ISSN: 1540-8140.

Abstract | Links | BibTeX

Borst, Andrew J; Weidle, Connor E; Gray, Matthew D; Frenz, Brandon; Snijder, Joost; Joyce, M Gordon; Georgiev, Ivelin S; Stewart-Jones, Guillaume Be; Kwong, Peter D; McGuire, Andrew T; DiMaio, Frank; Stamatatos, Leonidas; Pancera, Marie; Veesler, David

Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core Journal Article

In: Elife, vol. 7, 2018, ISSN: 2050-084X.

Abstract | Links | BibTeX

Chen, Zhen; Suzuki, Hiroshi; Kobayashi, Yuki; Wang, Ashley C; DiMaio, Frank; Kawashima, Shigehiro A; Walz, Thomas; Kapoor, Tarun M

Structural Insights into Mdn1, an Essential AAA Protein Required for Ribosome Biogenesis Journal Article

In: Cell, vol. 175, no. 3, pp. 822–834.e18, 2018, ISSN: 1097-4172.

Abstract | Links | BibTeX

Cianfrocco, Michael A; Lahiri, Indrajit; DiMaio, Frank; Leschziner, Andres E

cryoem-cloud-tools: A software platform to deploy and manage cryo-EM jobs in the cloud Journal Article

In: J Struct Biol, vol. 203, no. 3, pp. 230–235, 2018, ISSN: 1095-8657.

Abstract | Links | BibTeX

Kellogg, Elizabeth H; Hejab, Nisreen M A; Poepsel, Simon; Downing, Kenneth H; DiMaio, Frank; Nogales, Eva

Near-atomic model of microtubule-tau interactions Journal Article

In: Science, vol. 360, no. 6394, pp. 1242–1246, 2018, ISSN: 1095-9203.

Abstract | Links | BibTeX

Park, Hahnbeom; Ovchinnikov, Sergey; Kim, David E; DiMaio, Frank; Baker, David

Protein homology model refinement by large-scale energy optimization Journal Article

In: Proc Natl Acad Sci U S A, vol. 115, no. 12, pp. 3054–3059, 2018, ISSN: 1091-6490.

Abstract | Links | BibTeX

Lu, Peilong; Min, Duyoung; DiMaio, Frank; Wei, Kathy Y; Vahey, Michael D; Boyken, Scott E; Chen, Zibo; Fallas, Jorge A; Ueda, George; Sheffler, William; Mulligan, Vikram Khipple; Xu, Wenqing; Bowie, James U; Baker, David

Accurate computational design of multipass transmembrane proteins Journal Article

In: Science, vol. 359, no. 6379, pp. 1042–1046, 2018, ISSN: 1095-9203.

Abstract | Links | BibTeX

Usluer, Gülsima D; DiMaio, Frank; Yang, Shun Kai; Hansen, Jesse M; Polka, Jessica K; Mullins, R Dyche; Kollman, Justin M

Cryo-EM structure of the bacterial actin AlfA reveals unique assembly and ATP-binding interactions and the absence of a conserved subdomain Journal Article

In: Proc Natl Acad Sci U S A, vol. 115, no. 13, pp. 3356–3361, 2018, ISSN: 1091-6490.

Abstract | Links | BibTeX

Ovchinnikov, Sergey; Park, Hahnbeom; Kim, David E; DiMaio, Frank; Baker, David

Protein structure prediction using Rosetta in CASP12 Journal Article

In: Proteins, vol. 86 Suppl 1, no. Suppl 1, pp. 113–121, 2018, ISSN: 1097-0134.

Abstract | Links | BibTeX

Park, Hahnbeom; Kim, David E; Ovchinnikov, Sergey; Baker, David; DiMaio, Frank

Automatic structure prediction of oligomeric assemblies using Robetta in CASP12 Journal Article

In: Proteins, vol. 86 Suppl 1, no. Suppl 1, pp. 283–291, 2018, ISSN: 1097-0134.

Abstract | Links | BibTeX

2017

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

Structural basis for the initiation of eukaryotic transcription-coupled DNA repair Journal Article

In: Nature, vol. 551, no. 7682, pp. 653–657, 2017, ISSN: 1476-4687.

Abstract | Links | BibTeX

Borst, Andrew J; James, Zachary M; Zagotta, William N; Ginsberg, Mark; Rey, Felix A; DiMaio, Frank; Backovic, Marija; Veesler, David

The Therapeutic Antibody LM609 Selectively Inhibits Ligand Binding to Human αβ Integrin via Steric Hindrance Journal Article

In: Structure, vol. 25, no. 11, pp. 1732–1739.e5, 2017, ISSN: 1878-4186.

Abstract | Links | BibTeX

Martin, Gregory M; Kandasamy, Balamurugan; DiMaio, Frank; Yoshioka, Craig; Shyng, Show-Ling

Anti-diabetic drug binding site in a mammalian K channel revealed by Cryo-EM Journal Article

In: Elife, vol. 6, 2017, ISSN: 2050-084X.

Abstract | Links | BibTeX

Ve, Thomas; Vajjhala, Parimala R; Hedger, Andrew; Croll, Tristan; DiMaio, Frank; Horsefield, Shane; Yu, Xiong; Lavrencic, Peter; Hassan, Zahid; Morgan, Garry P; Mansell, Ashley; Mobli, Mehdi; O’Carroll, Ailis; Chauvin, Brieuc; Gambin, Yann; Sierecki, Emma; Landsberg, Michael J; Stacey, Katryn J; Egelman, Edward H; Kobe, Bostjan

Structural basis of TIR-domain-assembly formation in MAL- and MyD88-dependent TLR4 signaling Journal Article

In: Nat Struct Mol Biol, vol. 24, no. 9, pp. 743–751, 2017, ISSN: 1545-9985.

Abstract | Links | BibTeX

Schoebel, Stefan; Mi, Wei; Stein, Alexander; Ovchinnikov, Sergey; Pavlovicz, Ryan; DiMaio, Frank; Baker, David; Chambers, Melissa G; Su, Huayou; Li, Dongsheng; Rapoport, Tom A; Liao, Maofu

Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3 Journal Article

In: Nature, vol. 548, no. 7667, pp. 352–355, 2017, ISSN: 1476-4687.

Abstract | Links | BibTeX

Frenz, Brandon; Walls, Alexandra C; Egelman, Edward H; Veesler, David; DiMaio, Frank

RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps Journal Article

In: Nat Methods, vol. 14, no. 8, pp. 797–800, 2017, ISSN: 1548-7105.

Abstract | Links | BibTeX

Kasson, Peter; DiMaio, Frank; Yu, Xiong; Lucas-Staat, Soizick; Krupovic, Mart; Schouten, Stefan; Prangishvili, David; Egelman, Edward H

Model for a novel membrane envelope in a filamentous hyperthermophilic virus Journal Article

In: Elife, vol. 6, 2017, ISSN: 2050-084X.

Abstract | Links | BibTeX

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

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design Journal Article

In: J Chem Theory Comput, vol. 13, no. 6, pp. 3031–3048, 2017, ISSN: 1549-9626.

Abstract | Links | BibTeX

James, Zachary M; Borst, Andrew J; Haitin, Yoni; Frenz, Brandon; DiMaio, Frank; Zagotta, William N; Veesler, David

CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel Journal Article

In: Proc Natl Acad Sci U S A, vol. 114, no. 17, pp. 4430–4435, 2017, ISSN: 1091-6490.

Abstract | Links | BibTeX

Marze, Nicholas A; Jeliazkov, Jeliazko R; Burman, Shourya S Roy; Boyken, Scott E; DiMaio, Frank; Gray, Jeffrey J

Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35 Journal Article

In: Proteins, vol. 85, no. 3, pp. 479–486, 2017, ISSN: 1097-0134.

Abstract | Links | BibTeX

DiMaio, Frank

Rosetta Structure Prediction as a Tool for Solving Difficult Molecular Replacement Problems Journal Article

In: Methods Mol Biol, vol. 1607, pp. 455–466, 2017, ISSN: 1940-6029.

Abstract | Links | BibTeX

Walls, Alexandra; Tortorici, M Alejandra; Bosch, Berend-Jan; Frenz, Brandon; Rottier, Peter J M; DiMaio, Frank; Rey, Felix A; Veesler, David

Crucial steps in the structure determination of a coronavirus spike glycoprotein using cryo-electron microscopy Journal Article

In: Protein Sci, vol. 26, no. 1, pp. 113–121, 2017, ISSN: 1469-896X.

Abstract | Links | BibTeX

2016

Park, Hahnbeom; Bradley, Philip; Greisen, Per; Liu, Yuan; Mulligan, Vikram Khipple; Kim, David E; Baker, David; DiMaio, Frank

Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules Journal Article

In: J Chem Theory Comput, vol. 12, no. 12, pp. 6201–6212, 2016, ISSN: 1549-9626.

Abstract | Links | BibTeX

Fu, Tian-Min; Li, Yang; Lu, Alvin; Li, Zongli; Vajjhala, Parimala R; Cruz, Anthony C; Srivastava, Devendra B; DiMaio, Frank; Penczek, Pawel A; Siegel, Richard M; Stacey, Katryn J; Egelman, Edward H; Wu, Hao

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

In: Mol Cell, vol. 64, no. 2, pp. 236–250, 2016, ISSN: 1097-4164.

Abstract | Links | BibTeX

Walls, Alexandra C; Tortorici, M Alejandra; Frenz, Brandon; Snijder, Joost; Li, Wentao; Rey, Félix A; DiMaio, Frank; Bosch, Berend-Jan; Veesler, David

Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy Journal Article

In: Nat Struct Mol Biol, vol. 23, no. 10, pp. 899–905, 2016, ISSN: 1545-9985.

Abstract | Links | BibTeX

Wang, Ray Yu-Ruei; Song, Yifan; Barad, Benjamin A; Cheng, Yifan; Fraser, James S; DiMaio, Frank

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

In: Elife, vol. 5, 2016, ISSN: 2050-084X.

Abstract | Links | BibTeX

Ovchinnikov, Sergey; Kim, David E; Wang, Ray Yu-Ruei; Liu, Yuan; DiMaio, Frank; Baker, David

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

In: Proteins, vol. 84 Suppl 1, no. Suppl 1, pp. 67–75, 2016, ISSN: 1097-0134.

Abstract | Links | BibTeX

Park, Hahnbeom; DiMaio, Frank; Baker, David

CASP11 refinement experiments with ROSETTA Journal Article

In: Proteins, vol. 84 Suppl 1, no. Suppl 1, pp. 314–322, 2016, ISSN: 1097-0134.

Abstract | Links | BibTeX

Park, Hahnbeom; DiMaio, Frank; Baker, David

CASP11 refinement experiments with ROSETTA Journal Article

In: Proteins, vol. 84 Suppl 1, no. Suppl 1, pp. 314–322, 2016, ISSN: 1097-0134.

Abstract | Links | BibTeX

Bender, Brian J; Cisneros, Alberto; Duran, Amanda M; Finn, Jessica A; Fu, Darwin; Lokits, Alyssa D; Mueller, Benjamin K; Sangha, Amandeep K; Sauer, Marion F; Sevy, Alexander M; Sliwoski, Gregory; Sheehan, Jonathan H; DiMaio, Frank; Meiler, Jens; Moretti, Rocco

Protocols for Molecular Modeling with Rosetta3 and RosettaScripts Journal Article

In: Biochemistry, vol. 55, no. 34, pp. 4748–4763, 2016, ISSN: 1520-4995.

Abstract | Links | BibTeX

Conway, Patrick; DiMaio, Frank

Improving hybrid statistical and physical forcefields through local structure enumeration Journal Article

In: Protein Sci, vol. 25, no. 8, pp. 1525–1534, 2016, ISSN: 1469-896X.

Abstract | Links | BibTeX

Boyken, Scott E; Chen, Zibo; Groves, Benjamin; Langan, Robert A; Oberdorfer, Gustav; Ford, Alex; Gilmore, Jason M; Xu, Chunfu; DiMaio, Frank; Pereira, Jose Henrique; Sankaran, Banumathi; Seelig, Georg; Zwart, Peter H; Baker, David

De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity Journal Article

In: Science, vol. 352, no. 6286, pp. 680–687, 2016, ISSN: 1095-9203.

Abstract | Links | BibTeX

Walls, Alexandra C; Tortorici, M Alejandra; Bosch, Berend-Jan; Frenz, Brandon; Rottier, Peter J M; DiMaio, Frank; Rey, Félix A; Veesler, David

Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer Journal Article

In: Nature, vol. 531, no. 7592, pp. 114–117, 2016, ISSN: 1476-4687.

Abstract | Links | BibTeX

DiMaio, F; Chiu, W

Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps Journal Article

In: Methods Enzymol, vol. 579, pp. 255–276, 2016, ISSN: 1557-7988.

Abstract | Links | BibTeX

Hospenthal, Manuela K; Redzej, Adam; Dodson, Karen; Ukleja, Marta; Frenz, Brandon; Rodrigues, Catarina; Hultgren, Scott J; DiMaio, Frank; Egelman, Edward H; Waksman, Gabriel

Structure of a Chaperone-Usher Pilus Reveals the Molecular Basis of Rod Uncoiling Journal Article

In: Cell, vol. 164, no. 1-2, pp. 269–278, 2016, ISSN: 1097-4172.

Abstract | Links | BibTeX

Hospenthal, Manuela K; Redzej, Adam; Dodson, Karen; Ukleja, Marta; Frenz, Brandon; Rodrigues, Catarina; Hultgren, Scott J; DiMaio, Frank; Egelman, Edward H; Waksman, Gabriel

Structure of a Chaperone-Usher Pilus Reveals the Molecular Basis of Rod Uncoiling Journal Article

In: Cell, vol. 164, no. 1-2, pp. 269–278, 2016, ISSN: 1097-4172.

Abstract | Links | BibTeX

2015

King, Indigo Chris; Gleixner, James; Doyle, Lindsey; Kuzin, Alexandre; Hunt, John F; Xiao, Rong; Montelione, Gaetano T; Stoddard, Barry L; DiMaio, Frank; Baker, David

Precise assembly of complex beta sheet topologies from de novo designed building blocks Journal Article

In: Elife, vol. 4, 2015, ISSN: 2050-084X.

Abstract | Links | BibTeX

King, Indigo Chris; Gleixner, James; Doyle, Lindsey; Kuzin, Alexandre; Hunt, John F; Xiao, Rong; Montelione, Gaetano T; Stoddard, Barry L; DiMaio, Frank; Baker, David

Precise assembly of complex beta sheet topologies from de novo designed building blocks Journal Article

In: Elife, vol. 4, 2015, ISSN: 2050-084X.

Abstract | Links | BibTeX

Barad, Benjamin A; Echols, Nathaniel; Wang, Ray Yu-Ruei; Cheng, Yifan; DiMaio, Frank; Adams, Paul D; Fraser, James S

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

In: Nat Methods, vol. 12, no. 10, pp. 943–946, 2015, ISSN: 1548-7105.

Abstract | Links | BibTeX

Barad, Benjamin A; Echols, Nathaniel; Wang, Ray Yu-Ruei; Cheng, Yifan; DiMaio, Frank; Adams, Paul D; Fraser, James S

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

In: Nat Methods, vol. 12, no. 10, pp. 943–946, 2015, ISSN: 1548-7105.

Abstract | Links | BibTeX

DiMaio, Frank; Chen, Chun-Chieh; Yu, Xiong; Frenz, Brandon; Hsu, Yau-Heiu; Lin, Na-Sheng; Egelman, Edward H

The molecular basis for flexibility in the flexible filamentous plant viruses Journal Article

In: Nat Struct Mol Biol, vol. 22, no. 8, pp. 642–644, 2015, ISSN: 1545-9985.

Abstract | Links | BibTeX

Matthaei, James F; DiMaio, Frank; Richards, Jeffrey J; Pozzo, Lilo D; Baker, David; Baneyx, François

Designing Two-Dimensional Protein Arrays through Fusion of Multimers and Interface Mutations Journal Article

In: Nano Lett, vol. 15, no. 8, pp. 5235–5239, 2015, ISSN: 1530-6992.

Abstract | Links | BibTeX

Blok, Neil B; Tan, Dongyan; Wang, Ray Yu-Ruei; Penczek, Pawel A; Baker, David; DiMaio, Frank; Rapoport, Tom A; Walz, Thomas

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

In: Proc Natl Acad Sci U S A, vol. 112, no. 30, pp. E4017–E4025, 2015, ISSN: 1091-6490.

Abstract | Links | BibTeX

Gonen, Shane; DiMaio, Frank; Gonen, Tamir; Baker, David

Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces Journal Article

In: Science, vol. 348, no. 6241, pp. 1365–1368, 2015, ISSN: 1095-9203.

Abstract | Links | BibTeX

Park, Hahnbeom; DiMaio, Frank; Baker, David

The origin of consistent protein structure refinement from structural averaging Journal Article

In: Structure, vol. 23, no. 6, pp. 1123–1128, 2015, ISSN: 1878-4186.

Abstract | Links | BibTeX

DiMaio, Frank; Yu, Xiong; Rensen, Elena; Krupovic, Mart; Prangishvili, David; Egelman, Edward H

Virology. A virus that infects a hyperthermophile encapsidates A-form DNA Journal Article

In: Science, vol. 348, no. 6237, pp. 914–917, 2015, ISSN: 1095-9203.

Abstract | Links | BibTeX

DiMaio, Frank; Song, Yifan; Li, Xueming; Brunner, Matthias J; Xu, Chunfu; Conticello, Vincent; Egelman, Edward; Marlovits, Thomas; Cheng, Yifan; Baker, David

Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement Journal Article

In: Nat Methods, vol. 12, no. 4, pp. 361–365, 2015, ISSN: 1548-7105.

Abstract | Links | BibTeX

Wang, Ray Yu-Ruei; Kudryashev, Mikhail; Li, Xueming; Egelman, Edward H; Basler, Marek; Cheng, Yifan; Baker, David; DiMaio, Frank

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

In: Nat Methods, vol. 12, no. 4, pp. 335–338, 2015, ISSN: 1548-7105.

Abstract | Links | BibTeX

Solomonson, Matthew; Setiaputra, Dheva; Makepeace, Karl A T; Lameignere, Emilie; Petrotchenko, Evgeniy V; Conrady, Deborah G; Bergeron, Julien R; Vuckovic, Marija; DiMaio, Frank; Borchers, Christoph H; Yip, Calvin K; Strynadka, Natalie C J

Structure of EspB from the ESX-1 type VII secretion system and insights into its export mechanism Journal Article

In: Structure, vol. 23, no. 3, pp. 571–583, 2015, ISSN: 1878-4186.

Abstract | Links | BibTeX

O’Meara, Matthew J; Leaver-Fay, Andrew; Tyka, Michael D; Stein, Amelie; Houlihan, Kevin; DiMaio, Frank; Bradley, Philip; Kortemme, Tanja; Baker, David; Snoeyink, Jack; Kuhlman, Brian

Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta Journal Article

In: J Chem Theory Comput, vol. 11, no. 2, pp. 609–622, 2015, ISSN: 1549-9626.

Abstract | Links | BibTeX

Kudryashev, Mikhail; Wang, Ray Yu-Ruei; Brackmann, Maximilian; Scherer, Sebastian; Maier, Timm; Baker, David; DiMaio, Frank; Stahlberg, Henning; Egelman, Edward H; Basler, Marek

Structure of the type VI secretion system contractile sheath Journal Article

In: Cell, vol. 160, no. 5, pp. 952–962, 2015, ISSN: 1097-4172.

Abstract | Links | BibTeX

Egelman, E H; Xu, C; DiMaio, F; Magnotti, E; Modlin, C; Yu, X; Wright, E; Baker, D; Conticello, V P

Structural plasticity of helical nanotubes based on coiled-coil assemblies Journal Article

In: Structure, vol. 23, no. 2, pp. 280–289, 2015, ISSN: 1878-4186.

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2014

Huang, Po-Ssu; Oberdorfer, Gustav; Xu, Chunfu; Pei, Xue Y; Nannenga, Brent L; Rogers, Joseph M; DiMaio, Frank; Gonen, Tamir; Luisi, Ben; Baker, David

High thermodynamic stability of parametrically designed helical bundles Journal Article

In: Science, vol. 346, no. 6208, pp. 481–485, 2014, ISSN: 1095-9203.

Abstract | Links | BibTeX

Gawarzewski, Iris; DiMaio, Frank; Winterer, Elisa; Tschapek, Britta; Smits, Sander H J; Jose, Joachim; Schmitt, Lutz

Crystal structure of the transport unit of the autotransporter adhesin involved in diffuse adherence from Escherichia coli Journal Article

In: J Struct Biol, vol. 187, no. 1, pp. 20–29, 2014, ISSN: 1095-8657.

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Wagner, Ulrike Gabriella; DiMaio, Frank; Kolkenbrock, Stephan; Fetzner, Susanne

Crystal structure analysis of EstA from Arthrobacter sp. Rue61a–an insight into catalytic promiscuity Journal Article

In: FEBS Lett, vol. 588, no. 7, pp. 1154–1160, 2014, ISSN: 1873-3468.

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Kim, David E; Dimaio, Frank; Wang, Ray Yu-Ruei; Song, Yifan; Baker, David

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

In: Proteins, vol. 82 Suppl 2, no. 0 2, pp. 208–218, 2014, ISSN: 1097-0134.

Abstract | Links | BibTeX

Conway, Patrick; Tyka, Michael D; DiMaio, Frank; Konerding, David E; Baker, David

Relaxation of backbone bond geometry improves protein energy landscape modeling Journal Article

In: Protein Sci, vol. 23, no. 1, pp. 47–55, 2014, ISSN: 1469-896X.

Abstract | Links | BibTeX

2013

DiMaio, Frank

Advances in Rosetta structure prediction for difficult molecular-replacement problems Journal Article

In: Acta Crystallogr D Biol Crystallogr, vol. 69, no. Pt 11, pp. 2202–2208, 2013, ISSN: 1399-0047.

Abstract | Links | BibTeX

DiMaio, Frank; Echols, Nathaniel; Headd, Jeffrey J; Terwilliger, Thomas C; Adams, Paul D; Baker, David

Improved low-resolution crystallographic refinement with Phenix and Rosetta Journal Article

In: Nat Methods, vol. 10, no. 11, pp. 1102–1104, 2013, ISSN: 1548-7105.

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Song, Yifan; DiMaio, Frank; Wang, Ray Yu-Ruei; Kim, David; Miles, Chris; Brunette, Tj; Thompson, James; Baker, David

High-resolution comparative modeling with RosettaCM Journal Article

In: Structure, vol. 21, no. 10, pp. 1735–1742, 2013, ISSN: 1878-4186.

Abstract | Links | BibTeX

Brelidze, Tinatin I; Gianulis, Elena C; DiMaio, Frank; Trudeau, Matthew C; Zagotta, William N

Structure of the C-terminal region of an ERG channel and functional implications Journal Article

In: Proc Natl Acad Sci U S A, vol. 110, no. 28, pp. 11648–11653, 2013, ISSN: 1091-6490.

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DiMaio, Frank; Zhang, Junjie; Chiu, Wah; Baker, David

Cryo-EM model validation using independent map reconstructions Journal Article

In: Protein Sci, vol. 22, no. 6, pp. 865–868, 2013, ISSN: 1469-896X.

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Bergeron, Julien R C; Worrall, Liam J; Sgourakis, Nikolaos G; DiMaio, Frank; Pfuetzner, Richard A; Felise, Heather B; Vuckovic, Marija; Yu, Angel C; Miller, Samuel I; Baker, David; Strynadka, Natalie C J

A refined model of the prototypical Salmonella SPI-1 T3SS basal body reveals the molecular basis for its assembly Journal Article

In: PLoS Pathog, vol. 9, no. 4, pp. e1003307, 2013, ISSN: 1553-7374.

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Adams, Paul D; Baker, David; Brunger, Axel T; Das, Rhiju; DiMaio, Frank; Read, Randy J; Richardson, David C; Richardson, Jane S; Terwilliger, Thomas C

Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems Journal Article

In: Annu Rev Biophys, vol. 42, pp. 265–287, 2013, ISSN: 1936-1238.

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2012

Alon, Assaf; Grossman, Iris; Gat, Yair; Kodali, Vamsi K; DiMaio, Frank; Mehlman, Tevie; Haran, Gilad; Baker, David; Thorpe, Colin; Fass, Deborah

The dynamic disulphide relay of quiescin sulphydryl oxidase Journal Article

In: Nature, vol. 488, no. 7411, pp. 414–418, 2012, ISSN: 1476-4687.

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Terwilliger, Thomas C; Dimaio, Frank; Read, Randy J; Baker, David; Bunkóczi, Gábor; Adams, Paul D; Grosse-Kunstleve, Ralf W; Afonine, Pavel V; Echols, Nathaniel

phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta Journal Article

In: J Struct Funct Genomics, vol. 13, no. 2, pp. 81–90, 2012, ISSN: 1570-0267.

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Bankston, John R; Camp, Stacey S; DiMaio, Frank; Lewis, Alan S; Chetkovich, Dane M; Zagotta, William N

Structure and stoichiometry of an accessory subunit TRIP8b interaction with hyperpolarization-activated cyclic nucleotide-gated channels Journal Article

In: Proc Natl Acad Sci U S A, vol. 109, no. 20, pp. 7899–7904, 2012, ISSN: 1091-6490.

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2011

Gilski, Miroslaw; Kazmierczyk, Maciej; Krzywda, Szymon; Zábranská, Helena; Cooper, Seth; Popović, Zoran; Khatib, Firas; DiMaio, Frank; Thompson, James; Baker, David; Pichová, Iva; Jaskolski, Mariusz

High-resolution structure of a retroviral protease folded as a monomer Journal Article

In: Acta Crystallogr D Biol Crystallogr, vol. 67, no. Pt 11, pp. 907–914, 2011, ISSN: 1399-0047.

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Khatib, Firas; DiMaio, Frank; ; ; Cooper, Seth; Kazmierczyk, Maciej; Gilski, Miroslaw; Krzywda, Szymon; Zabranska, Helena; Pichova, Iva; Thompson, James; Popović, Zoran; Jaskolski, Mariusz; Baker, David

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

In: Nat Struct Mol Biol, vol. 18, no. 10, pp. 1175–1177, 2011, ISSN: 1545-9985.

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Valkov, Eugene; Stamp, Anna; Dimaio, Frank; Baker, David; Verstak, Brett; Roversi, Pietro; Kellie, Stuart; Sweet, Matthew J; Mansell, Ashley; Gay, Nicholas J; Martin, Jennifer L; Kobe, Bostjan

Crystal structure of Toll-like receptor adaptor MAL/TIRAP reveals the molecular basis for signal transduction and disease protection Journal Article

In: Proc Natl Acad Sci U S A, vol. 108, no. 36, pp. 14879–14884, 2011, ISSN: 1091-6490.

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Zhang, Junjie; Ma, Boxue; DiMaio, Frank; Douglas, Nicholai R; Joachimiak, Lukasz A; Baker, David; Frydman, Judith; Levitt, Michael; Chiu, Wah

Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure Journal Article

In: Structure, vol. 19, no. 5, pp. 633–639, 2011, ISSN: 1878-4186.

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Lyskowski, Andrzej; Oeemig, Jesper S; Jaakkonen, Anniina; Rommi, Katariina; DiMaio, Frank; Zhou, Dongwen; Kajander, Tommi; Baker, David; Wlodawer, Alexander; Goldman, Adrian; Iwaï, Hideo

Cloning, expression, purification, crystallization and preliminary X-ray diffraction data of the Pyrococcus horikoshii RadA intein Journal Article

In: Acta Crystallogr Sect F Struct Biol Cryst Commun, vol. 67, no. Pt 5, pp. 623–626, 2011, ISSN: 1744-3091.

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DiMaio, Frank; Terwilliger, Thomas C; Read, Randy J; Wlodawer, Alexander; Oberdorfer, Gustav; Wagner, Ulrike; Valkov, Eugene; Alon, Assaf; Fass, Deborah; Axelrod, Herbert L; Das, Debanu; Vorobiev, Sergey M; Iwaï, Hideo; Pokkuluri, P Raj; Baker, David

Improved molecular replacement by density- and energy-guided protein structure optimization Journal Article

In: Nature, vol. 473, no. 7348, pp. 540–543, 2011, ISSN: 1476-4687.

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Sgourakis, Nikolaos G; Lange, Oliver F; DiMaio, Frank; André, Ingemar; Fitzkee, Nicholas C; Rossi, Paolo; Montelione, Gaetano T; Bax, Ad; Baker, David

Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings Journal Article

In: J Am Chem Soc, vol. 133, no. 16, pp. 6288–6298, 2011, ISSN: 1520-5126.

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Li, Mi; Dimaio, Frank; Zhou, Dongwen; Gustchina, Alla; Lubkowski, Jacek; Dauter, Zbigniew; Baker, David; Wlodawer, Alexander

Crystal structure of XMRV protease differs from the structures of other retropepsins Journal Article

In: Nat Struct Mol Biol, vol. 18, no. 2, pp. 227–229, 2011, ISSN: 1545-9985.

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DiMaio, Frank; Leaver-Fay, Andrew; Bradley, Phil; Baker, David; André, Ingemar

Modeling symmetric macromolecular structures in Rosetta3 Journal Article

In: PLoS One, vol. 6, no. 6, pp. e20450, 2011, ISSN: 1932-6203.

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Chen, Dong-Hua; Baker, Matthew L; Hryc, Corey F; DiMaio, Frank; Jakana, Joanita; Wu, Weimin; Dougherty, Matthew; Haase-Pettingell, Cameron; Schmid, Michael F; Jiang, Wen; Baker, David; King, Jonathan A; Chiu, Wah

Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus Journal Article

In: Proc Natl Acad Sci U S A, vol. 108, no. 4, pp. 1355–1360, 2011, ISSN: 1091-6490.

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Tyka, Michael D; Keedy, Daniel A; André, Ingemar; Dimaio, Frank; Song, Yifan; Richardson, David C; Richardson, Jane S; Baker, David

Alternate states of proteins revealed by detailed energy landscape mapping Journal Article

In: J Mol Biol, vol. 405, no. 2, pp. 607–618, 2011, ISSN: 1089-8638.

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2010

Baker, Matthew L; Baker, Mariah R; Hryc, Corey F; Dimaio, Frank

Analyses of subnanometer resolution cryo-EM density maps Journal Article

In: Methods Enzymol, vol. 483, pp. 1–29, 2010, ISSN: 1557-7988.

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2009

DiMaio, Frank; Tyka, Michael D; Baker, Matthew L; Chiu, Wah; Baker, David

Refinement of protein structures into low-resolution density maps using rosetta Journal Article

In: J Mol Biol, vol. 392, no. 1, pp. 181–190, 2009, ISSN: 1089-8638.

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Raman, Srivatsan; Vernon, Robert; Thompson, James; Tyka, Michael; Sadreyev, Ruslan; Pei, Jimin; Kim, David; Kellogg, Elizabeth; DiMaio, Frank; Lange, Oliver; Kinch, Lisa; Sheffler, Will; Kim, Bong-Hyun; Das, Rhiju; Grishin, Nick V; Baker, David

Structure prediction for CASP8 with all-atom refinement using Rosetta Journal Article

In: Proteins, vol. 77 Suppl 9, no. 0 9, pp. 89–99, 2009, ISSN: 1097-0134.

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DiMaio, Frank P; Soni, Ameet B; Phillips, George N; Shavlik, Jude W

Spherical-harmonic decomposition for molecular recognition in electron-density maps Journal Article

In: Int J Data Min Bioinform, vol. 3, no. 2, pp. 205–227, 2009, ISSN: 1748-5673.

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2007

DiMaio, Frank; Kondrashov, Dmitry A; Bitto, Eduard; Soni, Ameet; Bingman, Craig A; Phillips, George N; Shavlik, Jude W

Creating protein models from electron-density maps using particle-filtering methods Journal Article

In: Bioinformatics, vol. 23, no. 21, pp. 2851–2858, 2007, ISSN: 1367-4811.

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2006

DiMaio, Frank; Shavlik, Jude; Phillips, George N

A probabilistic approach to protein backbone tracing in electron density maps Journal Article

In: Bioinformatics, vol. 22, no. 14, pp. e81–e89, 2006, ISSN: 1367-4811.

Abstract | Links | BibTeX