Publications

2019

J. Park, A.C. Walls, Z. Wang, M.M. Sauer, W. Li, M.A. M.A. Tortorici, B.J. Bosch, F. DiMaio, D. Veesler (2019). Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors. Nat Struct Mol Biol. doi: 10.1038/s41594-019-0334-7.

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. H.M. Berman, P.D. Adams, A.A. Bonvin, S.K. Burley, B. Carragher, W. Chiu, DiMaio, T.E. Ferrin, M.J. Gabanyi, T.D. Goddard, P.R. Griffin, J. Haas, C.A. Hanke, J.C. Hoch, G. Hummer, G. Kurisu, C.L. Lawson, A. Leitner, J.L. Markley, J. Meiler, G.T. Montelione, G.N. Phillips Jr, T. Prisner, J. Rappsilber, D.C. Schriemer, T. Schwede, C.A.M. Seidel, T.S. Strutzenberg, D.I. Svergun, E. Tajkhorshid, J. Trewhella, B. Vallat, S. Velankar, G.W. Vuister, B. Webb, J.D. Westbrook, K.L. White, A. Sali (2019). Structure. 227(12):1745-1759.

E. Park, L. Zhang, J.K. Bang, T. Andresson, F. DiMaio, K.S. Lee (2019). Phase separation of Polo-like kinase 4 by autoactivation and clustering drives centriole biogenesis. Nat Commun. 10(1):4959.

T. Chou, L. Apelt, D.P. Farrell, S.R. White, J. Woodsmith, V. Svetlov, J.S. Goldstein, A.R. Nager, Z. Li, J. Muller, H. Dollfus, E. Nudler, U. Stelzl, F. DiMaio, M.V. Nachury, T. Walz (2019). The Molecular Architecture of Native BBSome Obtained by an Integrated Structural Approach. Structure. 27(9):1384-1394.
†co-corresponding

Dai, T.K. Aman, F. DiMaio, W.N. Zagotta (2019). The HCN channel voltage sensor undergoes a large downward motion during hyperpolarization. Nat Struct Mol Biol. 26(8):686-694.

Lahiri, J. Xu, B.G. Han, J. Oh, D. Wang, F. DiMaio, A.E. Leschziner (2019). 3.1 Å structure of yeast RNA polymerase II elongation complex stalled at a cyclobutane pyrimidine dimer lesion solved using streptavidin affinity grids.  J Struct Biol. 207(3):270-278.

Koepnick, J. Flatten, T. Husain, A. Ford, D.A. Silva, M.J. Bick, A. Bauer, G. Liu, Y. Ishida, A. Boykov, R.D. Estep, S. Kleinfelter, T. Nørgård-Solano, L. Wei, F. Players, G.T. Montelione, F. DiMaio, Z. Popović, F. Khatib, S. Cooper, D. Baker (2019). De novo protein design by citizen scientists. Nature. 570(7761):390-394.

N. Rizo, J. Lin, S.N. Gates, E. Tse, S.M. Bart, L.M. Castellano, F. DiMaio, J. Shorter, D.R. Southworth (2019). Structural basis for substrate gripping and translocation by the ClpB AAA+ disaggregase.  Nat Commun. 10(1):2393.

L. Ilca, X. Sun, K. El Omari, A. Kotecha, F. de Haas, F. DiMaio, J.M. Grimes, D.I. Stuart, M.M. Poranen, J.T. Huiskonen (2019). Multiple liquid crystalline geometries of highly compacted nucleic acid in a dsRNA virus. Nature. 570(7760):252-256.

Wang, V. Cvirkaite-Krupovic, M.A.B. Kreutzberger, Z. Su, G.A.P. de Oliveira, T. Osinski, N. Sherman, F. DiMaio, J.S. Wall, D. Prangishvili, M. Krupovic, E.H. Egelman (2019). An extensively glycosylated archaeal pilus survives extreme conditions. Nat Microbiol. 4(8):1401-1410.

Chen, M.C. Johnson, J. Chen, M.J. Bick, S.E. Boyken, B. Lin, J.J. De Yoreo, J.M. Kollman, D. Baker, F. DiMaio (2019). Self-Assembling 2D Arrays with de Novo Protein Building Blocks. J Am Chem Soc. 141(22):8891-8895.

Chen, S. Boyken, M. Jia, F. Busch, D. Flores-Solis, M. Bick, P. Lu, Z. Van Aernum, A Sahasrabuddhe, R. Langan, S. Bermeo, T.J. Brunette, V. Mulligan, L. Carter, F. DiMaio, N. Sgourakis, V. Wysocki, D. Baker (2019). Programmable design of orthogonal protein heterodimers. Nature 565(7737):106-111.

Frenz, S. Rämisch, A. Borst, A. Walls, J. Adolf-Bryfogle, W. Schief, D. Veesler, F. DiMaio (2019). Automatically fixing errors in glycoprotein structures with Rosetta. Structure: 27(1):134-139.


2018

Park, K.D. Lacourse, C. Cambillau, F. DiMaio, J. Mougous, D. Veesler (2018). Structure of the type VI secretion system TssK-TssF-TssG baseplate subcomplex revealed by cryo-electron microscopy. Nature Communication 9(1):5385.

Borst, C. Weidle, M. Gray, B. Frenz, J. Snijder, M. Joyce, I. Georgiev, G. Stewart-Jones, P. Kwong, A. McGuire, F. DiMaio, L. Stamatatos, M. Pancera, D. Veesler. Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core. Elife e37688.

Sui, H. Arlt, K.P. Brock, Z. Lai, F. DiMaio, D. Marks, M. Liao, R. Farese, T. Walther. Cryo-electron microscopy structure of the lipid droplet-formation protein seipin. J Cell Biol 217(12):4080-4091.

Chen, H. Suzuki, Y. Kobayashi, A.C. Wang, F. DiMaio, S.A. Kawashima, T. Walz, T.M. Kapoor. Structural Insights into Mdn1, an Essential AAA Protein Required for Ribosome Biogenesis. Cell. 2018 175(3):822-834.e18.

Kellogg, N. Hejab, S. Poepsel, K. Downing, F. DiMaio, E. Nogales (2018). Near-atomic model of microtubule-tau interactions. Science.  doi: 10.1126/science.aat1780.

Cianfrocco, I. Lahiri, F. DiMaio, A. Leschziner (2018). cryoem-cloud-tools: A software platform to deploy and manage cryo-EM jobs in the cloud.  J Struct Biol. doi: 10.1016/j.jsb.2018.05.014.

Usluer, F. DiMaio, S. Yang, J. Hansen, J. Polka, R. Mullins, J. Kollman (2018). Cryo-EM structure of the bacterial actin AlfA reveals unique assembly and ATP-binding interactions and the absence of a conserved subdomain. Proc Natl Acad Sci. doi: 10.1073/pnas.1715836115.

Park, S. Ovchinnikov, D. Kim, F. DiMaio, D. Baker (2018). Protein homology model refinement by large-scale energy optimization. Proc Natl Acad Sci.  doi: 10.1073/pnas.1719115115.

Lu, D. Min, F. DiMaio, K. Wei, M. Vahey, S. Boyken, Z. Chen, J. Fallas, G. Ueda, W. Sheffler, V. Mulligan, W. Xu, J. Bowie, D. Baker (2018). Accurate computational design of multipass transmembrane proteins. Science 359:1042-1046.

Ovchinnikov, H. Park, D. Kim, F. DiMaio, D. Baker (2018). Protein structure prediction using Rosetta in CASP12. Proteins 86 Suppl 1:113-121.

Park, D. Kim, S. Ovchinnikov, D. Baker, F. DiMaio (2018). Automatic structure prediction of oligomeric assemblies using Robetta in CASP12. Proteins. 86 Suppl 1:283-291.


2017

Xu, I. Lahiri, W. Wang, A. Wier, M. Cianfrocco, J. Chong, A. Hare, P. Dervan, F. DiMaio, A. Leschziner, D. Wang (2017). Structural basis for the initiation of eukaryotic transcription-coupled DNA repair.  Nature 551:653-657.

Borst, Z. James, W. Zagotta, M. Ginsberg, F. Rey, F. DiMaio, M. Backovic, D. Veesler (2017). The Therapeutic Antibody LM609 Selectively Inhibits Ligand Binding to Human αVβ3 Integrin via Steric Hindrance. Structure. 25:1732-1739.

Martin, B. Kandasamy, F. DiMaio, C. Yoshioka, S. Shyng. Anti-diabetic drug binding site in a mammalian KATP channel revealed by Cryo-EM.  Elife e31054.

Park, D. Kim, S. Ovchinnikov, D. Baker, F. DiMaio (2017). Automatic structure prediction of oligomeric assemblies using Robetta in CASP 12.  Proteins. doi: 10.1002/prot.25387

Schoebel, W. Mi, A. Stein, S. Ovchinnikov, R. Pavlovicz, F. DiMaio, D. Baker, M.G. Chambers, H. Su, D. Li, T.A. Rapoport, M. Liao (2017). Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3. Nature. 2017 548(7667): 352-355.

Frenz, A. Walls, E. Egelman, D. Veesler, F. DiMaio (2017). A greedy conformational sampling strategy enables automated interpretation of difficult cryoEM maps.  Nature Methods 14(8):797-800.

Ve, P.R. Vajjhala, A. Hedger, T. Croll, F. DiMaio, S. Horsefield, X. Yu, P. Lavrencic, Z. Hassan, G.P. Morgan, A. Mansell, M. Mobli, A. O’Carroll, B. Chauvin, Y. Gambin, E. Sierecki, M.J. Landsberg, K.J. Stacey, E.H. Egelman, B. Kobe (2017). Structural basis of TIR-domain-assembly formation in MAL- and MyD88-dependent TLR4 signaling. Nat Struct Mol Biol 24(9):743-751.

Kasson, F. DiMaio, X. Yu, S. Lucas-Staat, M. Krupovic, S. Schouten, D. Prangishvili, E.H. Egelman (2017). Model for a novel membrane envelope in a filamentous hyperthermophilic virus. Elife. 6:e26268.

F. Alford, A. Leaver-Fay, J.R. Jeliazkov, M.J. O’Meara, F. DiMaio, H. Park, M. Shapovalov, P. Renfrew, V. Mulligan, K. Kappel, J. Labonte, M. Pacella, R. Bonneau, P. Bradley, R. Dunbrack, R. Das, D. Baker, B. Kuhlman, T. Kortemme, J. Gray (2017). The Rosetta all-atom energy function for macromolecular modeling and design. J Chem Theory Comput. doi: 10.1021/acs.jctc.7b00125.

James, A. Borst, Y. Haitin, B. Frenz, F. DiMaio, W. Zagotta, D. Veesler (2017). CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel. Proc Natl Acad Sci. 114(17):4430-4435.

Marze, J. Jeliazkov, S. Roy Burman, S. Boyken, F. DiMaio, J. Gray (2017). Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35.  Proteins 85(3):479-486.

Walls, M. Tortorici, B. Bosch, B. Frenz, P.J. Rottier, F. DiMaio, F. Rey, D. Veesler (2017). Crucial steps in the structure determination of a coronavirus spike glycoprotein using cryo-electron microscopy.  Protein Sci. 26(1):113-121.


2016

Park, P. Bradley, P. Greisen, Y. Liu, V. Mulligan, D. Kim, D. Baker, F. DiMaio (2016). Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules. J Chem Theory Comput. 13;12(12):6201-6212.

Fu, Y. Li, A. Lu, Z. Li, P. Vajjhala, A. Cruz, D. Srivastava, F. DiMaio, P. Penczek, R. Siegel, K. Stacey, E. Egelman, H. Wu (2016). Cryo-EM Structure of Caspase-8 Tandem DED Filament Reveals Assembly and Regulation Mechanisms of the Death-Inducing Signaling Complex.  Mol Cell 64(2):236-250.

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. e17219.

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. 12(12):6201-6212.

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.

S. Ovchinnikov, D.E. Kim, R.Y. Wang, Y. Liu, F. DiMaio, D. Baker (2016). Improved de novo structure prediction in CASP11 by incorporating Co-evolution information into rosetta. Proteins. Suppl 1:67-75.


2015

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. E11012.

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. Proc Natl Acad Sci. 112(30):E4017-25.

B. Barad, N. Echols, R. Wang, Y. Cheng, F. DiMaio, P. Adams and J. Fraser (2015). EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy. Nature Methods. 12(10):943-6.

F. DiMaio, C.C. Chen, X. Yu, B. Frenz, Y.H. Hsu, N.S. Lin and E. Egelman (2015). The molecular basis for flexibility in the flexible filamentous plant viruses. Nature Structural & Molecular Biology. 22(8):642-4.

A. Sali, H.M. Berman, T. Schwede, J. Trewhella, G. Kleywegt, S.K. Burley, J. Markley, H. Nakamura, P. Adams, A.M. Bonvin, W. Chiu, M.D. Peraro, DiMaio, T.E. Ferrin, K. Grünewald, A. Gutmanas, R. Henderson, G. Hummer, K. Iwasaki, G. Johnson, C.L. Lawson, J. Meiler, M.A. Marti-Renom, G.T. Montelione, M. Nilges, R. Nussinov, A. Patwardhan, J. Rappsilber, R.J. Read, H. Saibil, G.F. Schröder, C.D. Schwieters, C.A. Seidel, D. Svergun, M. Topf, E.L. Ulrich, S. Velankar and J.D. Westbrook (2015). Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure. S0969-2126(15)00194-X.

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

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

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

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

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

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

R. Y.-R. Wang, M. Kudryashev, X. Li, E. Egelman, M. Basler, Y. Cheng, D. Baker and F. DiMaio (2015). De novo protein structure determination from near-atomic-resolution Cryo-EM Maps.  Nature Methods. 12(4):335-8.

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

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

M. Solomonson, D. Setiaputra, K. Makepeace, E. Lameignere, E. Petrotchenko, D. Conrady, J. Bergeron, M. Vuckovic, F. DiMaio, C. Borchers, C. Yip, and N. Strynadka. (2015) Structure of the Mycobacterium tuberculosis ESX-1-secreted virulence factor EspB and insights into its export mechanism.  Structure. 23(3):571-83.


2014

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

I. Gawarzewski, F. DiMaio, E. Winterer, B. Tschapek, S.H. Smits, J. Jose and L. Schmitt (2014). Crystal structure of the transport unit of the autotransporter dhesion involved in diffuse adherence from Escherichia coli. J Struct Biol. 187(1):20-9.

U.G. Wagner, F. DiMaio, S. Kolkenbrock and S. Fetzner (2014). Crystal structure analysis of EstA from Arthrobacter sp. Rue61a—an insight into catalytic promiscuity. FEBS Lett. 588(7):1154-60.

P. Conway, M. Tyka, F. DiMaio†, D. Konerding and D. Baker (2014). Relaxation of backbone bond geometry improves protein energy landscape modeling. Protein Science. 23:47-55.
†contributed equally

D. Kim, F. DiMaio†, R. Y.-R. Wang, Y. Song, D. Baker (2014). One contact for every twelve residues is sufficient for accurate topology-level protein structure modeling. Proteins. 82:208-18.
†contributed equally


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. 10:1102-4.
†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. 21:1735-42.
†contributed equally

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

F. DiMaio, J. Zhang, W. Chiu, D.Baker (2013). CryoEM model evaluation using independent datasets. Protein Science. 22:865-8.

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 (PNAS). 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, 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 (PNAS). 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 (PNAS). 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 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 and older

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 (PNAS). 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.

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; also presented at the Fourteenth International Conference on Intelligent Systems for Molecular Biology (ISMB), Fortaleza, Brazil (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.