Publications

2016

R. Wang, Y. Song, B. Barad, Y. Cheng, J. Fraser, F. DiMaio (2016). Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife (in press).

H. Park, P. Bradley, P. Greisen, Y. Liu, V. Mulligan, D. Kim, D. Baker, F. DiMaio (2016). Simultaneous optimization of biomolecular energy function on features from small molecules and macromolecules. Journal of Chemical Theory and Computation (in press).

A. Walls, M. Tortorici, B. Frenz, J. Snijder, W. Li, F. Rey, F. DiMaio, B. Bosch, D. Veesler (2016). Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy. Nature Structural & Molecular Biology. 23, 899–905.

B.J. Bender, A. Cisneros, A.M. Duran, J.A. Finn, D. Fu, A.D. Lokits, B.K. Mueller, A.K. Sangha, M.F. Sauer, A.M. Sevy, G. Sliwoski, J.H. Sheehan, F. DiMaio, J. Meiler, R. Moretti. (2016). Protocols for Molecular Modeling with Rosetta3 and RosettaScripts. Biochemistry. 55 (34): 4748– 4763.

P. Conway, F. DiMaio (2016). Improving hybrid statistical and physical forcefields through local structure enumeration. Protein Sci. 25(8):1525-34.

A.C. Walls, M.A. Tortorici, B.J. Bosch, B. Frenz, P.J. Rottier, F. DiMaio, F.A. Rey, D. Veesler (2016). Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer. Nature 531(7592):114-7.

M.K. Hospenthal, A. Redzej, K. Dodson, M. Ukleja, B. Frenz, C. Rodrigues, S.J. Hultgren, F. DiMaio, E.H. Egelman, G. Waksman (2016). Structure of a Chaperone-Usher Pilus Reveals the Molecular Basis of Rod Uncoiling. Cell. 164(1-2):269-78.


2015

S. Ovchinnikov, D.E. Kim, R.Y. Wang, Y. Liu, F. DiMaio, D. Baker (2015). Improved de novo structure prediction in CASP11 by incorporating Co-evolution information into rosetta. Proteins. doi: 10.1002/prot.24974.

I.C. King, J. Gleixner, L. Doyle, A. Kuzin, J.F. Hunt, R. Xiao, G.T. Montelione, B.L. Stoddard, F. DiMaio, D. Baker (2015). Precise assembly of complex beta sheet topologies from de novo designed building blocks. Elife. doi: 10.7554/eLife.11012.

N. Blok, D. Tan, R. Wang, P. Pencek, D. Baker, F. DiMaio, T. Rapoport and T. Walz (2015). Structure determination of the peroxisomal Pex1/Pex6 ATPase complex from 7Å cryoEM maps. Proceedings of the National Academy of Sciences (PNAS). 112(30):E4017-25.

Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F,  Adams PD, Fraser JS. EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.  Nature Methods. 2015; 12(10):943-6.

Matthaei JF, DiMaio F, Richards JJ, Pozzo LD, Baker D, Baneyx F.   Designing Two-Dimensional Protein Arrays through Fusion of Multimers and Interface Mutations.
Nano letters. 2015; 15(8):5235-9.

DiMaio F, Chen CC, Yu X, Frenz B, Hsu YH, Lin NS, Egelman EH.  The molecular basis for flexibility in the flexible filamentous plant viruses. Nature Structural & Molecular Biology. 2015; 22(8):642-4.

Park H, DiMaio F, Baker D.  CASP11 refinement experiments with ROSETTA.  Proteins. 2015;

Gonen S, DiMaio F, Gonen T, Baker D.  Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces.  Science . 2015; 348(6241):1365-8.

Park H, DiMaio F, Baker D.  The origin of consistent protein structure refinement from structural averaging.  Structure. 2015; 23(6):1123-8.

DiMaio F, Yu X, Rensen E, Krupovic M, Prangishvili D, Egelman E.  A virus that infects a hyperthermophile encapsidates A-form DNA.  Science. 2015; 348(6237):914-7.

DiMaio F, Song Y, Li X, Brunner MJ, Xu C, Conticello V, Egelman E, Marlovits TC, Cheng Y, Baker D.  Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement.   Nature Methods. 2015; 12(4):361-5.

Wang RY, Kudryashev M, Li X, Egelman EH, Basler M, Cheng Y, Baker D, DiMaio F.  De novo protein structure determination from near-atomic-resolution cryo-EM maps.  Nature Methods. 2015; 12(4):335-8.

Solomonson M, Setiaputra D, Makepeace KA, Lameignere E, Petrotchenko EV, Conrady DG, Bergeron JR, Vuckovic M, DiMaio F, Borchers CH, Yip CK, Strynadka NC.  Structure of EspB from the ESX-1 type VII secretion system and insights into its export mechanism.  Structure. 2015; 23(3):571-83.

Kudryashev M, Wang RY, Brackmann M, Scherer S, Maier T, Baker D, DiMaio F, Stahlberg H, Egelman EH, Basler M.  Structure of the type VI secretion system contractile sheath. Cell. 2015; 160(5):952-62.

Egelman EH, Xu C, DiMaio F, Magnotti E, Modlin C, Yu X, Wright E, Baker D, Conticello VP.   Structural plasticity of helical nanotubes based on coiled-coil assemblies. Structure . 2015; 23(2):280-9.

O’Meara MJ, Leaver-Fay A, Tyka M, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B.  A Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta.  Journal of chemical theory and computation. 2015; 11(2):609-622.


2014

Huang PS, Oberdorfer G, Xu C, Pei XY, Nannenga BL, Rogers JM, DiMaio F, Gonen T, Luisi B, Baker D.  High thermodynamic stability of parametrically designed helical bundles.
Science. 2014; 346(6208):481-5.

Gawarzewski I, DiMaio F, Winterer E, Tschapek B, Smits SH, Jose J, Schmitt L.  Crystal structure of the transport unit of the autotransporter adhesin involved in diffuse adherence from Escherichia coli.  Journal of structural biology. 2014; 187(1):20-9.

Wagner UG, DiMaio F, Kolkenbrock S, Fetzner S.  Crystal structure analysis of EstA from Arthrobacter sp. Rue61a–an insight into catalytic promiscuity. FEBS letters. 2014; 588(7):1154-60.

Kim DE, DiMaio F, Yu-Ruei Wang R, Song Y, Baker D.  One contact for every twelve residues allows robust and accurate topology-level protein structure modeling.  Proteins. 2014; 82 Suppl 2:208-18.

Conway P, Tyka MD, DiMaio F, Konerding DE, Baker D.  Relaxation of backbone bond geometry improves protein energy landscape modeling.  Protein Science. 2014; 23(1):47-55.


2013

DiMaio F.  Advances in Rosetta structure prediction for difficult molecular-replacement problems.  Acta crystallographica D. 2013; 69(Pt 11):2202-8.

DiMaio F, Echols N, Headd JJ, Terwilliger TC, Adams PD, Baker D.  Improved low-resolution crystallographic refinement with Phenix and Rosetta.  Nature Methods. 2013; 10(11):1102-4.

Song Y, DiMaio F, Wang RY, Kim D, Miles C, Brunette T, Thompson J, Baker D.  High-resolution comparative modeling with RosettaCM.  Structure. 2013; 21(10):1735-42.

Brelidze TI, Gianulis EC, DiMaio F, Trudeau MC, Zagotta WN.  Structure of the C-terminal region of an ERG channel and functional implications.  Proceedings of the National Academy of Sciences. 2013; 110(28):11648-53.

DiMaio F, Zhang J, Chiu W, Baker D.  Cryo-EM model validation using independent map reconstructions.  Protein Science. 2013; 22(6):865-8.

Adams PD, Baker D, Brunger AT, Das R, DiMaio F, Read RJ, Richardson DC, Richardson JS, Terwilliger TC.  Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems.  Annual review of biophysics. 2013; 42:265-87.

Bergeron JR, Worrall LJ, Sgourakis NG, DiMaio F, Pfuetzner RA, Felise HB, Vuckovic M, Yu AC, Miller SI, Baker D, Strynadka NC.  A refined model of the prototypical Salmonella SPI-1 T3SS basal body reveals the molecular basis for its assembly. PLoS pathogens. 2013; 9(4):e1003307.


2012

Alon A, Grossman I, Gat Y, Kodali VK, DiMaio F, Mehlman T, Haran G, Baker D, Thorpe C, Fass D.  The dynamic disulphide relay of quiescin sulphydryl oxidase. Nature. 2012; 488(7411):414-8.

Terwilliger TC, DiMaio F, Read RJ, Baker D, Bunkóczi G, Adams PD, Grosse-Kunstleve RW, Afonine PV, Echols N.  phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.  Journal of structural and functional genomics. 2012; 13(2):81-90.

Bankston JR, Camp SS, DiMaio F, Lewis AS, Chetkovich DM, Zagotta WN.  Structure and stoichiometry of an accessory subunit TRIP8b interaction with hyperpolarization-activated cyclic nucleotide-gated channels.  Proceedings of the National Academy of Sciences. 2012; 109(20):7899-904.


2011

Gilski M, Kazmierczyk M, Krzywda S, Zábranská H, Cooper S, Popović Z, Khatib F, DiMaio F, Thompson J, Baker D, Pichová I, Jaskolski M.  High-resolution structure of a retroviral protease folded as a monomer.  Acta crystallographica D. 2011; 67(Pt 11):907-14.
PubMed [journal]PMID: 22101816 PMCID: PMC3211970

Khatib F, DiMaio F, Cooper S, Kazmierczyk M, Gilski M, Krzywda S, Zabranska H, Pichova I, Thompson J, Popović Z, Jaskolski M, Baker D.  Crystal structure of a monomeric retroviral protease solved by protein folding game players.  Nature Structural & Molecular Biology. 2011; 18(10):1175-7.

Valkov E, Stamp A, Dimaio F, Baker D, Verstak B, Roversi P, Kellie S, Sweet MJ, Mansell A, Gay NJ, Martin JL, Kobe B.  Crystal structure of Toll-like receptor adaptor MAL/TIRAP reveals the molecular basis for signal transduction and disease protection. Proceedings of the National Academy of Sciences. 2011; 108(36):14879-84.

DiMaio F, Terwilliger TC, Read RJ, Wlodawer A, Oberdorfer G, Wagner U, Valkov E, Alon A, Fass D, Axelrod HL, Das D, Vorobiev SM, Iwaï H, Pokkuluri PR, Baker D.  Improved molecular replacement by density- and energy-guided protein structure optimization.  Nature. 2011; 473(7348):540-3.

Zhang J, Ma B, DiMaio F, Douglas NR, Joachimiak LA, Baker D, Frydman J, Levitt M, Chiu W.  Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure.  Structure. 2011; 19(5):633-9.

Lyskowski A, Oeemig JS, Jaakkonen A, Rommi K, DiMaio F, Zhou D, Kajander T, Baker D, Wlodawer A, Goldman A, Iwaï H.  Cloning, expression, purification, crystallization and preliminary X-ray diffraction data of the Pyrococcus horikoshii RadA intein.  Acta crystallographica F.   2011; 67(Pt 5):623-6.

Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings.  Sgourakis NG, Lange OF, DiMaio F, André I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D.  Journal of the American Chemical Society. 2011; 133(16):6288-98.

Li M, Dimaio F, Zhou D, Gustchina A, Lubkowski J, Dauter Z, Baker D, Wlodawer A.
Crystal structure of XMRV protease differs from the structures of other retropepsins.
Nature Structural & Molecular Biology. 2011; 18(2):227-9.

Chen DH, Baker ML, Hryc CF, DiMaio F, Jakana J, Wu W, Dougherty M, Haase-Pettingell C, Schmid MF, Jiang W, Baker D, King JA, Chiu W.  Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus.  Proceedings of the National Academy of Sciences. 2011; 108(4):1355-60.

Tyka MD, Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, Baker D.  Alternate states of proteins revealed by detailed energy landscape mapping.
Journal of molecular biology. 2011; 405(2):607-18.

DiMaio F, Leaver-Fay A, Bradley P, Baker D, André I.  Modeling symmetric macromolecular structures in Rosetta3.  PloS one. 2011; 6(6):e20450.


2010 and older

Baker ML, Baker MR, Hryc CF, DiMaio F.  Analyses of subnanometer resolution cryo-EM density maps.  Methods in enzymology. 2010; 483:1-29.

DiMaio F, Tyka MD, Baker ML, Chiu W, Baker D.  Refinement of protein structures into low-resolution density maps using rosetta.  Journal of molecular biology. 2009; 392(1):181-90.

DiMaio FP, Soni AB, Phillips GN Jr, Shavlik JW.  Spherical-harmonic decomposition for molecular recognition in electron-density maps.  International journal of data mining and bioinformatics. 2009; 3(2):205-27.

Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim BH, Das R, Grishin NV, Baker D.   Structure prediction for CASP8 with all-atom refinement using Rosetta.  Proteins. 2009; 77 Suppl 9:89-99.

DiMaio F, Kondrashov DA, Bitto E, Soni A, Bingman CA, Phillips GN Jr, Shavlik JW. Creating protein models from electron-density maps using particle-filtering methods.  Bioinformatics. 2007; 23(21):2851-8.

DiMaio F, Shavlik J, Phillips GN.  A probabilistic approach to protein backbone tracing in electron density maps.  Bioinformatics. 2006; 22(14):e81-9.