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Items: 1 to 50 of 88

1.

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

Cianfrocco MA, Lahiri I, DiMaio F, Leschziner AE.

J Struct Biol. 2018 Sep;203(3):230-235. doi: 10.1016/j.jsb.2018.05.014. Epub 2018 Jun 1.

PMID:
29864529
2.

Near-atomic model of microtubule-tau interactions.

Kellogg EH, Hejab NMA, Poepsel S, Downing KH, DiMaio F, Nogales E.

Science. 2018 Jun 15;360(6394):1242-1246. doi: 10.1126/science.aat1780. Epub 2018 May 10.

PMID:
29748322
3.

Protein homology model refinement by large-scale energy optimization.

Park H, Ovchinnikov S, Kim DE, DiMaio F, Baker D.

Proc Natl Acad Sci U S A. 2018 Mar 20;115(12):3054-3059. doi: 10.1073/pnas.1719115115. Epub 2018 Mar 5.

4.

Accurate computational design of multipass transmembrane proteins.

Lu P, Min D, DiMaio F, Wei KY, Vahey MD, Boyken SE, Chen Z, Fallas JA, Ueda G, Sheffler W, Mulligan VK, Xu W, Bowie JU, Baker D.

Science. 2018 Mar 2;359(6379):1042-1046. doi: 10.1126/science.aaq1739.

PMID:
29496880
5.

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

Usluer GD, DiMaio F, Yang SK, Hansen JM, Polka JK, Mullins RD, Kollman JM.

Proc Natl Acad Sci U S A. 2018 Mar 27;115(13):3356-3361. doi: 10.1073/pnas.1715836115. Epub 2018 Feb 13.

6.

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

Xu J, Lahiri I, Wang W, Wier A, Cianfrocco MA, Chong J, Hare AA, Dervan PB, DiMaio F, Leschziner AE, Wang D.

Nature. 2017 Nov 30;551(7682):653-657. doi: 10.1038/nature24658. Epub 2017 Nov 22.

7.

Anti-diabetic drug binding site in a mammalian KATP channel revealed by Cryo-EM.

Martin GM, Kandasamy B, DiMaio F, Yoshioka C, Shyng SL.

Elife. 2017 Oct 24;6. pii: e31054. doi: 10.7554/eLife.31054.

8.

The Therapeutic Antibody LM609 Selectively Inhibits Ligand Binding to Human αVβ3 Integrin via Steric Hindrance.

Borst AJ, James ZM, Zagotta WN, Ginsberg M, Rey FA, DiMaio F, Backovic M, Veesler D.

Structure. 2017 Nov 7;25(11):1732-1739.e5. doi: 10.1016/j.str.2017.09.007. Epub 2017 Oct 12.

PMID:
29033288
9.

Protein structure prediction using Rosetta in CASP12.

Ovchinnikov S, Park H, Kim DE, DiMaio F, Baker D.

Proteins. 2018 Mar;86 Suppl 1:113-121. doi: 10.1002/prot.25390. Epub 2017 Oct 8.

PMID:
28940798
10.

Automatic structure prediction of oligomeric assemblies using Robetta in CASP12.

Park H, Kim DE, Ovchinnikov S, Baker D, DiMaio F.

Proteins. 2018 Mar;86 Suppl 1:283-291. doi: 10.1002/prot.25387. Epub 2017 Oct 16.

11.

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

Ve T, Vajjhala PR, Hedger A, Croll T, DiMaio F, Horsefield S, Yu X, Lavrencic P, Hassan Z, Morgan GP, Mansell A, Mobli M, O'Carroll A, Chauvin B, Gambin Y, Sierecki E, Landsberg MJ, Stacey KJ, Egelman EH, Kobe B.

Nat Struct Mol Biol. 2017 Sep;24(9):743-751. doi: 10.1038/nsmb.3444. Epub 2017 Jul 31.

PMID:
28759049
12.

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

Schoebel S, Mi W, Stein A, Ovchinnikov S, Pavlovicz R, DiMaio F, Baker D, Chambers MG, Su H, Li D, Rapoport TA, Liao M.

Nature. 2017 Aug 17;548(7667):352-355. doi: 10.1038/nature23314. Epub 2017 Jul 6.

13.

Model for a novel membrane envelope in a filamentous hyperthermophilic virus.

Kasson P, DiMaio F, Yu X, Lucas-Staat S, Krupovic M, Schouten S, Prangishvili D, Egelman EH.

Elife. 2017 Jun 22;6. pii: e26268. doi: 10.7554/eLife.26268.

14.

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

Frenz B, Walls AC, Egelman EH, Veesler D, DiMaio F.

Nat Methods. 2017 Aug;14(8):797-800. doi: 10.1038/nmeth.4340. Epub 2017 Jun 19.

15.

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

DiMaio F.

Methods Mol Biol. 2017;1607:455-466. doi: 10.1007/978-1-4939-7000-1_19. Review.

PMID:
28573585
16.

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

Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL Jr, Das R, Baker D, Kuhlman B, Kortemme T, Gray JJ.

J Chem Theory Comput. 2017 Jun 13;13(6):3031-3048. doi: 10.1021/acs.jctc.7b00125. Epub 2017 May 12.

17.

CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel.

James ZM, Borst AJ, Haitin Y, Frenz B, DiMaio F, Zagotta WN, Veesler D.

Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):4430-4435. doi: 10.1073/pnas.1700248114. Epub 2017 Apr 10.

18.

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

Marze NA, Jeliazkov JR, Roy Burman SS, Boyken SE, DiMaio F, Gray JJ.

Proteins. 2017 Mar;85(3):479-486. doi: 10.1002/prot.25168. Epub 2016 Oct 24.

19.

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

Park H, Bradley P, Greisen P Jr, Liu Y, Mulligan VK, Kim DE, Baker D, DiMaio F.

J Chem Theory Comput. 2016 Dec 13;12(12):6201-6212. Epub 2016 Nov 7.

20.

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

Fu TM, Li Y, Lu A, Li Z, Vajjhala PR, Cruz AC, Srivastava DB, DiMaio F, Penczek PA, Siegel RM, Stacey KJ, Egelman EH, Wu H.

Mol Cell. 2016 Oct 20;64(2):236-250. doi: 10.1016/j.molcel.2016.09.009. Epub 2016 Oct 13.

21.

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

Walls A, Tortorici MA, Bosch BJ, Frenz B, Rottier PJ, DiMaio F, Rey FA, Veesler D.

Protein Sci. 2017 Jan;26(1):113-121. doi: 10.1002/pro.3048. Epub 2016 Oct 18.

22.

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

Wang RY, Song Y, Barad BA, Cheng Y, Fraser JS, DiMaio F.

Elife. 2016 Sep 26;5. pii: e17219. doi: 10.7554/eLife.17219.

23.

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

Walls AC, Tortorici MA, Frenz B, Snijder J, Li W, Rey FA, DiMaio F, Bosch BJ, Veesler D.

Nat Struct Mol Biol. 2016 Oct;23(10):899-905. doi: 10.1038/nsmb.3293. Epub 2016 Sep 12.

24.

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

DiMaio F, Chiu W.

Methods Enzymol. 2016;579:255-76. doi: 10.1016/bs.mie.2016.06.003. Epub 2016 Aug 12. Review.

25.

Protocols for Molecular Modeling with Rosetta3 and RosettaScripts.

Bender BJ, Cisneros A 3rd, Duran AM, Finn JA, Fu D, Lokits AD, Mueller BK, Sangha AK, Sauer MF, Sevy AM, Sliwoski G, Sheehan JH, DiMaio F, Meiler J, Moretti R.

Biochemistry. 2016 Aug 30;55(34):4748-63. doi: 10.1021/acs.biochem.6b00444. Epub 2016 Aug 16. Review.

26.

Improving hybrid statistical and physical forcefields through local structure enumeration.

Conway P, DiMaio F.

Protein Sci. 2016 Aug;25(8):1525-34. doi: 10.1002/pro.2956. Epub 2016 Jun 16.

27.

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

Boyken SE, Chen Z, Groves B, Langan RA, Oberdorfer G, Ford A, Gilmore JM, Xu C, DiMaio F, Pereira JH, Sankaran B, Seelig G, Zwart PH, Baker D.

Science. 2016 May 6;352(6286):680-7. doi: 10.1126/science.aad8865. Erratum in: Science. 2016 May 20;352(6288). pii: aag1318. doi: 10.1126/science.aag1318.

28.

Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer.

Walls AC, Tortorici MA, Bosch BJ, Frenz B, Rottier PJM, DiMaio F, Rey FA, Veesler D.

Nature. 2016 Mar 3;531(7592):114-117. doi: 10.1038/nature16988. Epub 2016 Feb 8.

29.

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

Hospenthal MK, Redzej A, Dodson K, Ukleja M, Frenz B, Rodrigues C, Hultgren SJ, DiMaio F, Egelman EH, Waksman G.

Cell. 2016 Jan 14;164(1-2):269-278. doi: 10.1016/j.cell.2015.11.049. Epub 2015 Dec 24.

30.

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

Ovchinnikov S, Kim DE, Wang RY, Liu Y, DiMaio F, Baker D.

Proteins. 2016 Sep;84 Suppl 1:67-75. doi: 10.1002/prot.24974. Epub 2016 Feb 24.

31.

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

King IC, Gleixner J, Doyle L, Kuzin A, Hunt JF, Xiao R, Montelione GT, Stoddard BL, DiMaio F, Baker D.

Elife. 2015 Dec 9;4. pii: e11012. doi: 10.7554/eLife.11012.

32.

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

Barad BA, Echols N, Wang RY, Cheng Y, DiMaio F, Adams PD, Fraser JS.

Nat Methods. 2015 Oct;12(10):943-6. doi: 10.1038/nmeth.3541. Epub 2015 Aug 17.

33.

CASP11 refinement experiments with ROSETTA.

Park H, DiMaio F, Baker D.

Proteins. 2016 Sep;84 Suppl 1:314-22. doi: 10.1002/prot.24862. Epub 2015 Aug 14.

34.

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

Blok NB, Tan D, Wang RY, Penczek PA, Baker D, DiMaio F, Rapoport TA, Walz T.

Proc Natl Acad Sci U S A. 2015 Jul 28;112(30):E4017-25. doi: 10.1073/pnas.1500257112. Epub 2015 Jul 13.

35.

The molecular basis for flexibility in the flexible filamentous plant viruses.

DiMaio F, Chen CC, Yu X, Frenz B, Hsu YH, Lin NS, Egelman EH.

Nat Struct Mol Biol. 2015 Aug;22(8):642-4. doi: 10.1038/nsmb.3054. Epub 2015 Jul 13.

36.

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

Gonen S, DiMaio F, Gonen T, Baker D.

Science. 2015 Jun 19;348(6241):1365-8. doi: 10.1126/science.aaa9897.

37.

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

DiMaio F, Yu X, Rensen E, Krupovic M, Prangishvili D, Egelman EH.

Science. 2015 May 22;348(6237):914-7. doi: 10.1126/science.aaa4181.

38.

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

Matthaei JF, DiMaio F, Richards JJ, Pozzo LD, Baker D, Baneyx F.

Nano Lett. 2015 Aug 12;15(8):5235-9. doi: 10.1021/acs.nanolett.5b01499. Epub 2015 May 26.

PMID:
25986921
39.

The origin of consistent protein structure refinement from structural averaging.

Park H, DiMaio F, Baker D.

Structure. 2015 Jun 2;23(6):1123-8. doi: 10.1016/j.str.2015.03.022. Epub 2015 May 7.

40.

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

O'Meara MJ, Leaver-Fay A, Tyka MD, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B.

J Chem Theory Comput. 2015 Feb 10;11(2):609-22. doi: 10.1021/ct500864r.

41.

Structure of the type VI secretion system contractile sheath.

Kudryashev M, Wang RY, Brackmann M, Scherer S, Maier T, Baker D, DiMaio F, Stahlberg H, Egelman EH, Basler M.

Cell. 2015 Feb 26;160(5):952-962. doi: 10.1016/j.cell.2015.01.037.

42.

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

DiMaio F, Song Y, Li X, Brunner MJ, Xu C, Conticello V, Egelman E, Marlovits T, Cheng Y, Baker D.

Nat Methods. 2015 Apr;12(4):361-365. doi: 10.1038/nmeth.3286. Epub 2015 Feb 23.

43.

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

Wang RY, Kudryashev M, Li X, Egelman EH, Basler M, Cheng Y, Baker D, DiMaio F.

Nat Methods. 2015 Apr;12(4):335-8. doi: 10.1038/nmeth.3287. Epub 2015 Feb 23.

44.

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

Solomonson M, Setiaputra D, Makepeace KAT, Lameignere E, Petrotchenko EV, Conrady DG, Bergeron JR, Vuckovic M, DiMaio F, Borchers CH, Yip CK, Strynadka NCJ.

Structure. 2015 Mar 3;23(3):571-583. doi: 10.1016/j.str.2015.01.002. Epub 2015 Feb 12.

45.

Structural plasticity of helical nanotubes based on coiled-coil assemblies.

Egelman EH, Xu C, DiMaio F, Magnotti E, Modlin C, Yu X, Wright E, Baker D, Conticello VP.

Structure. 2015 Feb 3;23(2):280-9. doi: 10.1016/j.str.2014.12.008. Epub 2015 Jan 22.

46.

High thermodynamic stability of parametrically designed helical bundles.

Huang PS, Oberdorfer G, Xu C, Pei XY, Nannenga BL, Rogers JM, DiMaio F, Gonen T, Luisi B, Baker D.

Science. 2014 Oct 24;346(6208):481-485. doi: 10.1126/science.1257481.

47.

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

Gawarzewski I, DiMaio F, Winterer E, Tschapek B, Smits SHJ, Jose J, Schmitt L.

J Struct Biol. 2014 Jul;187(1):20-29. doi: 10.1016/j.jsb.2014.05.003. Epub 2014 May 16.

PMID:
24841284
48.

Crystal structure analysis of EstA from Arthrobacter sp. Rue61a--an insight into catalytic promiscuity.

Wagner UG, DiMaio F, Kolkenbrock S, Fetzner S.

FEBS Lett. 2014 Apr 2;588(7):1154-60. doi: 10.1016/j.febslet.2014.02.045. Epub 2014 Mar 5.

49.

Relaxation of backbone bond geometry improves protein energy landscape modeling.

Conway P, Tyka MD, DiMaio F, Konerding DE, Baker D.

Protein Sci. 2014 Jan;23(1):47-55.

50.

Advances in Rosetta structure prediction for difficult molecular-replacement problems.

DiMaio F.

Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2202-8. doi: 10.1107/S0907444913023305. Epub 2013 Oct 12.

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