Publications

2013
  • F. DiMaio*, N. Echols*, J. Headd, T. Terwilliger, P. Adams, D. Baker (2013). Improved protein crystal structures at low resolution by integrated refinement with Phenix and Rosetta. Nature Methods (in press). *contributed equally
  • Y. Song*, F. DiMaio*, R. Y.-R. Wang, D. Kim, C. Miles, T.J. Brunette, J. Thompson and D. Baker (2013) High resolution comparative modeling with RosettaCM. Structure (in press). *contributed equally
  • D. Kim*, F. DiMaio*, R. Y.-R. Wang, Y. Song, D. Baker (2013). One contact for every twelve residues is sufficient for accurate topology-level protein structure modeling. Proteins (in press). *contributed equally
  • F. DiMaio (2013). Advances in Rosetta structure prediction for difficult molecular-replacement problems. Acta Crystallographica D (in press).
  • F. DiMaio, J. Zhang, W. Chiu, D.Baker (2013). CryoEM model evaluation using independent datasets. Protein Science. 22(6):865-8
  • T.I. Brelidze, E.C. Gianulis, F. DiMaio, M.C. Trudeau, W.N. Zagotta (2013). Structure of the C-terminal region of an ERG channel and functional implications. Proceedings of the National Academy of Sciences. 110:11648-53.
  • J. Bergeron, L. Worrall, N. Sgourakis, F. DiMaio, R. Pfuetzner, H. Felise, M. Vuckovic, A. Yu, S. Miller, D. Baker, N. Strynadka (2013). A Refined Model of the Prototypical Salmonella SPI-1 T3SS Basal Body Reveals the Molecular Basis for Its Assembly. PLoS Pathogens. 9:e1003307.
  • P. Adams, D. Baker, A. Brunger, R. Das, F. DiMaio, R. Read, D. Richardson, J. Richardson, T. Terwilliger (2013). Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems. Annu. Rev. Biophys. 42: 265-287.
2012
  • A. Alon, I. Grossman, Y. Gat, V. Kodali, F. DiMaio, T. Mehlman, G. Haran, D. Baker, C. Thorpe, D. Fass (2012). The dynamic disulphide relay of quiescin sulphydryl oxidase. Nature 488:414-8.
  • T. Terwilliger, F. DiMaio, R. Read, D. Baker, G. Bunkóczi, P. Adams, R. Grosse-Kunstleve, P. Afonine, N. Echols (2012). phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. J. Struct Funct Genomics. 13:81-90.
  • J. Bankston, S. Camp, F. DiMaio, A. Lewis, D. Chetkovich, W. Zagotta (2012). Structure and stoichiometry of an accessory subunit TRIP8b interaction with hyperpolarization- activated cyclic nucleotide-gated channels. Proceedings of the National Academy of Sciences. 109:7899-904.
2011
  • M. Gilski, M. Kazmierczyk, S. Krzywda, H. Zábranská, S. Cooper, Z. Popović, F. Khatib, F. F. DiMaio, J. Thompson, D. Baker, I. Pichová, M. Jaskolski. High-resolution structure of a retroviral protease folded as a monomer (2011). Acta Crystallographica D. 67:907-14.
  • F. Khatib, F. DiMaio, Foldit Contenders Group, Foldit Void Crushers Group, S. Cooper, M. Kazmierczyk, M. Gilski, S. Krzywda, H. Zabranska, I. Pichova, J. Thompson, Z. Popović, M. Jaskolski and D. Baker (2011). Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature Structural & Molecular Biology. 18:1175-7.
  • E. Valkov, A. Stamp, F. DiMaio, D. Baker, B. Verstak, P. Roversi, S. Kellie, M.J. Sweet, A. Mansell, N.J. Gay, J.L. Martin, and B. Kobe (2011). 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. 108:14879-84.
  • F. DiMaio, A. Leaver-Fay, P. Bradley, D. Baker, I. André. (2011) Modeling symmetric macromolecular structures in Rosetta3. PLoS One. 6:e20450.
  • J. Zhang, B. Ma, F. DiMaio, N. Douglas, L. Joachimiak, D. Baker, J. Frydman, M. Levitt, and W. Chiu (2011). Cryo-EM Structure of a Group II Chaperonin in the Prehydrolysis ATP- Bound State Leading to Lid Closure. Structure. 19:633-9.
  • F. DiMaio, T. Terwilliger, R. Read, A. Wlodawer, G. Oberdorfer, E. Valkov, A. Alon, D. Fass, H. Axelrod, D. Das, S. Vorobiev, H. Iwai, P. Pokkuluri and D. Baker (2011). Improving molecular replacement by density- and energy- guided protein structure optimization. Nature. 473:540-3.
  • A. Lyskowski, J.S. Oeemig, A. Jaakkonen, K. Rommi, F. DiMaio, D. Zhou, T. Kajander, D. Baker, A. Wlodawer, A. Goldman and H. Iwaï (2011). Cloning, expression, purification, crystallization and preliminary X-ray diffraction data of the Pyrococcus horikoshii RadA intein. Acta Crystallographica Sect. F. 67:623-6.
  • N. Sgourakis, O. Lange, F. DiMaio, I. André, N. Fitzkee, P. Rossi, G. Montelione, A. Bax, and D. Baker. (2011). Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings. Journal of the American Chemical Society. 133:6288-6298.
  • M. Li, F. DiMaio, D. Zhou, A. Gustchina, J. Lubkowski, Z. Dauter, D. Baker and A. Wlodawer (2011). Crystal structure of XMRV protease differs from the structures of other retropepsins. Nature Structural & Molecular Biology. 18:227-9.
2010
  • D.-H. Chen, M. Baker, C. Hryc, F. DiMaio, J. Jakana, W. Wu, M. Dougherty, C. Haase- Pettingell, M. Schmid, W. Jiang, D. Baker, J. King and W. Chiu (2010). Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proceedings of the National Academy of Sciences. 108:1355-60.
  • M. Tyka, D. Keedy, I. André, F. DiMaio, Y. Song, D. Richardson, J. Richardson and D. Baker (2010). Alternate states of proteins revealed by detailed energy landscape mapping. Journal of Molecular Biology. 405:607-18.
  • M.L. Baker, M.R. Baker, C. Hryc and F. DiMaio (2010). Analyses of subnanometer resolution cryo-EM density maps. Methods in Enzymology. 483:1-29.
2009 and older
  • F. DiMaio, M. Tyka, M. Baker, W. Chiu and D. Baker (2009). Refinement of protein structures into low-resolution density maps using Rosetta. Journal of Molecular Biology 392: 181-90.
  • S. Raman, R. Vernon, J. Thompson, M. Tyka, R. Sadreyev, J. Pei, D. Kim, E. Kellogg, F. DiMaio, O. Lange, L. Kinch, W. Sheffler, B. Kim, R. Das, N. Grishin and D. Baker. (2009) Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins 77:89-99.
  • F. DiMaio, A. Soni, G. Phillips and J. Shavlik (2009). Spherical-Harmonic Decomposition for Molecular Recognition in Electron-Density Maps. International Journal of Data Mining and Bioinformatics 3: 205-227.
  • F. DiMaio, D. Kondrashov, E. Bitto, A. Soni, C. Bingman, G. Phillips and J. Shavlik (2007). Creating Protein Models from Electron-Density Maps using Particle-Filtering Methods. Bioinformatics, 23: 2851-2858.
  • F. DiMaio, A. Soni, G. Phillips and J. Shavlik (2007). Improved Methods for Template- Matching in Electron-Density Maps Using Spherical Harmonics. Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, Fremont, CA.
  • F. DiMaio and J. Shavlik (2006). Belief propagation in large, highly connected graphs for 3D part-based object recognition. Proceedings of the Sixth IEEE International Conference on Data Mining (ICDM), Hong Kong.
  • F. DiMaio, J. Shavlik and G. Phillips (2006). A probabilistic approach to protein backbone tracing in electron density maps. Bioinformatics 22 (cited as a recommended article by Faculty of 1000).
  • F. DiMaio, J. Shavlik and G. Phillips (2005). Pictorial structures for molecular modeling: Interpreting density maps. Advances in Neural Information Processing Systems (NIPS) 17, Vancouver, Canada.
  • D. Gopan, F. DiMaio, N. Dor, T. Reps and M. Sagiv (2004). Numeric domains with summarized dimensions. Proceedings of Tools and Algorithms for the Construction and Analysis of Systems (TACAS), Barcelona, Spain.
  • F. DiMaio and J. Shavlik (2004). Learning an approximation to inductive Logic programming clause evaluation. Proceedings of the Fourteenth International Conference on Inductive Logic Programming, Porto, Portugal.