Year |
Citation |
Score |
2023 |
McShan AC, Flores-Solis D, Sun Y, Garfinkle SE, Toor JS, Young MC, Sgourakis NG. Conformational plasticity of RAS Q61 family of neoepitopes results in distinct features for targeted recognition. Nature Communications. 14: 8204. PMID 38081856 DOI: 10.1038/s41467-023-43654-9 |
0.708 |
|
2022 |
McShan AC, Devlin CA, Papadaki GF, Sun Y, Green AI, Morozov GI, Burslem GM, Procko E, Sgourakis NG. TAPBPR employs a ligand-independent docking mechanism to chaperone MR1 molecules. Nature Chemical Biology. PMID 35725941 DOI: 10.1038/s41589-022-01049-9 |
0.705 |
|
2021 |
McShan AC, Devlin CA, Morozov GI, Overall SA, Moschidi D, Akella N, Procko E, Sgourakis NG. TAPBPR promotes antigen loading on MHC-I molecules using a peptide trap. Nature Communications. 12: 3174. PMID 34039964 DOI: 10.1038/s41467-021-23225-6 |
0.712 |
|
2021 |
Nerli S, De Paula VS, McShan AC, Sgourakis NG. Backbone-independent NMR resonance assignments of methyl probes in large proteins. Nature Communications. 12: 691. PMID 33514730 DOI: 10.1038/s41467-021-20984-0 |
0.719 |
|
2020 |
O'Rourke SM, Morozov GI, Roberts JT, Barb AW, Sgourakis NG. Production of soluble pMHC-I molecules in mammalian cells using the molecular chaperone TAPBPR. Protein Engineering, Design & Selection : Peds. PMID 32725167 DOI: 10.1093/Protein/Gzaa015 |
0.345 |
|
2020 |
Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Sgourakis NG, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2 |
0.615 |
|
2020 |
Overall SA, Toor JS, Hao S, Yarmarkovich M, Sara M O'Rourke, Morozov GI, Nguyen S, Japp AS, Gonzalez N, Moschidi D, Betts MR, Maris JM, Smibert P, Sgourakis NG. High throughput pMHC-I tetramer library production using chaperone-mediated peptide exchange. Nature Communications. 11: 1909. PMID 32312993 DOI: 10.1038/S41467-020-15710-1 |
0.323 |
|
2020 |
Wei KY, Moschidi D, Bick MJ, Nerli S, McShan AC, Carter LP, Huang PS, Fletcher DA, Sgourakis NG, Boyken SE, Baker D. Computational design of closely related proteins that adopt two well-defined but structurally divergent folds. Proceedings of the National Academy of Sciences of the United States of America. PMID 32188784 DOI: 10.1073/Pnas.1914808117 |
0.785 |
|
2020 |
De Paula VS, Jude KM, Nerli S, Glassman CR, Garcia KC, Sgourakis NG. Interleukin-2 druggability is modulated by global conformational transitions controlled by a helical capping switch. Proceedings of the National Academy of Sciences of the United States of America. PMID 32184322 DOI: 10.1073/Pnas.2000419117 |
0.302 |
|
2019 |
Park J, Selvaraj B, McShan AC, Boyken SE, Wei KY, Oberdorfer G, DeGrado W, Sgourakis NG, Cuneo MJ, Myles DA, Baker D. De novo design of a homo-trimeric amantadine-binding protein. Elife. 8. PMID 31854299 DOI: 10.7554/Elife.47839 |
0.769 |
|
2019 |
McShan AC, Devlin CA, Overall SA, Park J, Toor JS, Moschidi D, Flores-Solis D, Choi H, Tripathi S, Procko E, Sgourakis NG. Molecular determinants of chaperone interactions on MHC-I for folding and antigen repertoire selection. Proceedings of the National Academy of Sciences of the United States of America. PMID 31796585 DOI: 10.1073/Pnas.1915562116 |
0.737 |
|
2019 |
Marceau AH, Brison CM, Nerli S, Arsenault HE, McShan AC, Chen E, Lee HW, Benanti JA, Sgourakis NG, Rubin SM. An order-to-disorder structural switch activates the FoxM1 transcription factor. Elife. 8. PMID 31134895 DOI: 10.7554/Elife.46131 |
0.701 |
|
2019 |
De Paula VS, Sgourakis NG, Francischetti IMB, Almeida FCL, Monteiro RQ, Valente AP. NMR structure determination of Ixolaris and Factor X interaction reveals a noncanonical mechanism of Kunitz inhibition. Blood. PMID 31133602 DOI: 10.1182/Blood.2018889493 |
0.334 |
|
2019 |
Chen Z, Boyken SE, Jia M, Busch F, Flores-Solis D, Bick MJ, Lu P, VanAernum ZL, Sahasrabuddhe A, Langan RA, Bermeo S, Brunette TJ, Mulligan VK, Carter LP, DiMaio F, ... Sgourakis NG, et al. Programmable design of orthogonal protein heterodimers. Nature. 565: 106-111. PMID 30568301 DOI: 10.1038/s41586-018-0802-y |
0.774 |
|
2019 |
Park J, Selvaraj B, McShan AC, Boyken SE, Wei KY, Oberdorfer G, DeGrado W, Sgourakis NG, Cuneo MJ, Myles DA, Baker D. Author response: De novo design of a homo-trimeric amantadine-binding protein Elife. DOI: 10.7554/Elife.47839.Sa2 |
0.737 |
|
2019 |
Marceau AH, Brison CM, Nerli S, Arsenault HE, McShan AC, Chen E, Lee H, Benanti JA, Sgourakis NG, Rubin SM. Author response: An order-to-disorder structural switch activates the FoxM1 transcription factor Elife. DOI: 10.7554/Elife.46131.032 |
0.682 |
|
2019 |
Mishra SH, Kancherla AK, Marincin K, Nerli S, Sgourakis N, Dowling D, Frueh DP. Structural Dynamics Couple Substrate-Induced Allosteric Responses with Domain Communication in Nonribosomal Peptide Synthetases Biophysical Journal. 116: 163a. DOI: 10.1016/J.Bpj.2018.11.908 |
0.314 |
|
2018 |
Nerli S, McShan AC, Sgourakis NG. Chemical shift-based methods in NMR structure determination. Progress in Nuclear Magnetic Resonance Spectroscopy. 106: 1-25. PMID 31047599 DOI: 10.1016/J.Pnmrs.2018.03.002 |
0.741 |
|
2018 |
Marcos E, Chidyausiku TM, McShan AC, Evangelidis T, Nerli S, Carter L, Nivón LG, Davis A, Oberdorfer G, Tripsianes K, Sgourakis NG, Baker D. De novo design of a non-local β-sheet protein with high stability and accuracy. Nature Structural & Molecular Biology. PMID 30374087 DOI: 10.1038/s41594-018-0141-6 |
0.764 |
|
2018 |
Natarajan K, Jiang J, May NA, Mage MG, Boyd LF, McShan AC, Sgourakis NG, Bax A, Margulies DH. The Role of Molecular Flexibility in Antigen Presentation and T Cell Receptor-Mediated Signaling. Frontiers in Immunology. 9: 1657. PMID 30065727 DOI: 10.3389/Fimmu.2018.01657 |
0.753 |
|
2018 |
McShan AC, Natarajan K, Kumirov VK, Flores-Solis D, Jiang J, Badstübner M, Toor JS, Bagshaw CR, Kovrigin EL, Margulies DH, Sgourakis NG. Peptide exchange on MHC-I by TAPBPR is driven by a negative allostery release cycle. Nature Chemical Biology. PMID 29988068 DOI: 10.1038/S41589-018-0096-2 |
0.72 |
|
2018 |
Toor JS, Rao AA, McShan AC, Yarmarkovich M, Nerli S, Yamaguchi K, Madejska AA, Nguyen S, Tripathi S, Maris JM, Salama SR, Haussler D, Sgourakis NG. A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations. Frontiers in Immunology. 9: 99. PMID 29441070 DOI: 10.3389/Fimmu.2018.00099 |
0.725 |
|
2018 |
Evangelidis T, Nerli S, Nováček J, Brereton AE, Karplus PA, Dotas RR, Venditti V, Sgourakis NG, Tripsianes K. Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra. Nature Communications. 9: 384. PMID 29374165 DOI: 10.1038/S41467-017-02592-Z |
0.36 |
|
2018 |
Morag O, Sgourakis NG, Abramov G, Goldbourt A. Filamentous Bacteriophage Viruses: Preparation, Magic-Angle Spinning Solid-State NMR Experiments, and Structure Determination. Methods in Molecular Biology (Clifton, N.J.). 1688: 67-97. PMID 29151205 DOI: 10.1007/978-1-4939-7386-6_4 |
0.378 |
|
2018 |
Marcos E, Chidyausiku TM, McShan AC, Evangelidis T, Nerli S, Carter L, Nivón LG, Davis A, Oberdorfer G, Tripsianes K, Sgourakis NG, Baker D. De novo design of a non-local beta-sheet protein with high stability and accuracy Nature Structural & Molecular Biology. 25: 1028-1034. DOI: 10.2210/Pdb6E5C/Pdb |
0.759 |
|
2018 |
Chen Z, Flores-Solis D, Sgourakis NG, Baker D. De Novo Design of a Protein Heterodimer with Specificity Mediated by Hydrogen Bond Networks Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb6Dmp/Pdb |
0.405 |
|
2018 |
Flores-Solis D, McShan A, Sgourakis N. Solution NMR Structure of Unbound P18-I10 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb6B9K/Pdb |
0.704 |
|
2018 |
Evangelidis T, Nerli S, Sgourakis NG, Tripsianes K. NMR solution structure of Rtt103 (RTT) protein using two 4D-spectra Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb5Woz/Pdb |
0.333 |
|
2018 |
Evangelidis T, Nerli S, Sgourakis NG, Tripsianes K. NMR solution structure of Enzyme I (nEIt) protein using two 4D-spectra Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb5Woy/Pdb |
0.317 |
|
2018 |
Evangelidis T, Nerli S, Sgourakis NG, Tripsianes K. NMR solution structure of KanY protein (ms6282) using two 4D-spectra Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb5Wox/Pdb |
0.309 |
|
2017 |
Natarajan K, McShan AC, Jiang J, Kumirov VK, Wang R, Zhao H, Schuck P, Tilahun ME, Boyd LF, Ying J, Bax A, Margulies DH, Sgourakis NG. An allosteric site in the T-cell receptor Cβ domain plays a critical signalling role. Nature Communications. 8: 15260. PMID 28508865 DOI: 10.1038/Ncomms15260 |
0.752 |
|
2015 |
Sgourakis NG, May NA, Boyd LF, Ying J, Bax A, Margulies DH. A Novel MHC-I Surface Targeted for Binding by the MCMV m06 Immunoevasin Revealed by Solution NMR. The Journal of Biological Chemistry. 290: 28857-68. PMID 26463211 DOI: 10.1074/Jbc.M115.689661 |
0.501 |
|
2015 |
Bergeron JRC, Sgourakis NG. Type IV Pilus: One architectural problem, many structural solutions Structure. 23: 253-255. PMID 25651057 DOI: 10.1016/J.Str.2015.01.004 |
0.329 |
|
2015 |
Morag O, Sgourakis NG, Baker D, Goldbourt A. The NMR-Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope. Proceedings of the National Academy of Sciences of the United States of America. 112: 971-6. PMID 25587134 DOI: 10.1073/Pnas.1415393112 |
0.461 |
|
2015 |
Sgourakis NG, Yau WM, Qiang W. Modeling an in-register, parallel "iowa" aβ fibril structure using solid-state NMR data from labeled samples with rosetta. Structure (London, England : 1993). 23: 216-27. PMID 25543257 DOI: 10.1016/J.Str.2014.10.022 |
0.363 |
|
2015 |
Bergeron JR, Worrall LJ, De S, Sgourakis NG, Cheung AH, Lameignere E, Okon M, Wasney GA, Baker D, McIntosh LP, Strynadka NC. The modular structure of the inner-membrane ring component PrgK facilitates assembly of the type III secretion system basal body. Structure (London, England : 1993). 23: 161-72. PMID 25533490 DOI: 10.1016/J.Str.2014.10.021 |
0.444 |
|
2015 |
Rossi P, Shi L, Liu G, Barbieri CM, Lee HW, Grant TD, Luft JR, Xiao R, Acton TB, Snell EH, Montelione GT, Baker D, Lange OF, Sgourakis NG. A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta. Proteins. 83: 309-17. PMID 25388768 DOI: 10.1002/Prot.24719 |
0.506 |
|
2014 |
Demers JP, Habenstein B, Loquet A, Kumar Vasa S, Giller K, Becker S, Baker D, Lange A, Sgourakis NG. High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy. Nature Communications. 5: 4976. PMID 25264107 DOI: 10.1038/Ncomms5976 |
0.482 |
|
2014 |
Sgourakis NG, Natarajan K, Ying J, Vogeli B, Boyd LF, Margulies DH, Bax A. The structure of mouse cytomegalovirus m04 protein obtained from sparse NMR data reveals a conserved fold of the m02-m06 viral immune modulator family. Structure (London, England : 1993). 22: 1263-1273. PMID 25126960 DOI: 10.1016/J.Str.2014.05.018 |
0.515 |
|
2014 |
Rossi P, Lange OF, Sgourakis NG, Song Y, Lee H, Aramini JM, Ertekin A, Xiao R, Acton TB, Baker D, Montelione GT. Solution NMR Structure of Maltose-binding protein from Escherichia coli, Northeast Structural Genomics Consortium (NESG) Target ER690 Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.2210/Pdb2Mv0/Pdb |
0.448 |
|
2013 |
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. 9: e1003307. PMID 23633951 DOI: 10.1371/Journal.Ppat.1003307 |
0.419 |
|
2013 |
Demers JP, Sgourakis NG, Gupta R, Loquet A, Giller K, Riedel D, Laube B, Kolbe M, Baker D, Becker S, Lange A. The common structural architecture of Shigella flexneri and Salmonella typhimurium type three secretion needles. Plos Pathogens. 9: e1003245. PMID 23555258 DOI: 10.1371/Journal.Ppat.1003245 |
0.461 |
|
2013 |
Rossi P, Sgourakis N, Shi L, Liu G, Barbieri C, Lee H, Grant T, Luft J, Xiao R, Acton T, Montelione G, Snell E, Baker D, Lange O. Solution structure of the Aha1 dimer from Colwellia psychrerythraea Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr19235 |
0.41 |
|
2013 |
Demers J, Sgourakis N, Gupta R, Loquet A, Giller K, Riedel D, Laube B, Kolbe M, Baker D, Becker S, Lange A. 13C and 15N chemical shifts for Shigella Flexneri MxiH Type three secretion system needle subunit Journal of Back and Musculoskeletal Rehabilitation. DOI: 10.13018/Bmr18651 |
0.333 |
|
2012 |
Lange OF, Rossi P, Sgourakis NG, Song Y, Lee HW, Aramini JM, Ertekin A, Xiao R, Acton TB, Montelione GT, Baker D. Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples. Proceedings of the National Academy of Sciences of the United States of America. 109: 10873-8. PMID 22733734 DOI: 10.1073/Pnas.1203013109 |
0.635 |
|
2012 |
Loquet A, Sgourakis NG, Gupta R, Giller K, Riedel D, Goosmann C, Griesinger C, Kolbe M, Baker D, Becker S, Lange A. Atomic model of the type III secretion system needle Nature. 486: 276-279. PMID 22699623 DOI: 10.1038/Nature11079 |
0.461 |
|
2012 |
Thompson JM, Sgourakis NG, Liu G, Rossi P, Tang Y, Mills JL, Szyperski T, Montelione GT, Baker D. Accurate protein structure modeling using sparse NMR data and homologous structure information. Proceedings of the National Academy of Sciences of the United States of America. 109: 9875-80. PMID 22665781 DOI: 10.1073/Pnas.1202485109 |
0.599 |
|
2012 |
Loquet A, Sgourakis NG, Gupta R, Giller K, Riedel D, Goosmann C, Griesinger C, Kolbe M, Baker D, Becker S, Lange A. Erratum: Corrigendum: Atomic model of the type III secretion system needle Nature. 488: 684-684. DOI: 10.1038/Nature11350 |
0.357 |
|
2011 |
Sgourakis NG, Lange OF, DiMaio F, André I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D. Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings. Journal of the American Chemical Society. 133: 6288-98. PMID 21466200 DOI: 10.1021/Ja111318M |
0.739 |
|
2011 |
Sgourakis NG, Merced-Serrano M, Boutsidis C, Drineas P, Du Z, Wang C, Garcia AE. Atomic-level characterization of the ensemble of the Aβ(1-42) monomer in water using unbiased molecular dynamics simulations and spectral algorithms. Journal of Molecular Biology. 405: 570-83. PMID 21056574 DOI: 10.1016/J.Jmb.2010.10.015 |
0.571 |
|
2010 |
Patel MM, Sgourakis NG, Garcia AE, Makhatadze GI. Experimental test of the thermodynamic model of protein cooperativity using temperature-induced unfolding of a Ubq-UIM fusion protein. Biochemistry. 49: 8455-67. PMID 20836541 DOI: 10.1021/Bi101163U |
0.563 |
|
2010 |
Zhuang W, Sgourakis NG, Li Z, Garcia AE, Mukamel S. Discriminating early stage A{beta}42 monomer structures using chirality-induced 2DIR spectroscopy in a simulation study. Proceedings of the National Academy of Sciences of the United States of America. 107: 15687-92. PMID 20798063 DOI: 10.1073/Pnas.1002131107 |
0.542 |
|
2010 |
Sgourakis NG, Garcia AE. The membrane complex between transducin and dark-state rhodopsin exhibits large-amplitude interface dynamics on the sub-microsecond timescale: insights from all-atom MD simulations. Journal of Molecular Biology. 398: 161-73. PMID 20184892 DOI: 10.1016/J.Jmb.2010.02.032 |
0.554 |
|
2010 |
Sgourakis NG, Patel MM, Garcia AE, Makhatadze GI, McCallum SA. Conformational dynamics and structural plasticity play critical roles in the ubiquitin recognition of a UIM domain. Journal of Molecular Biology. 396: 1128-44. PMID 20053359 DOI: 10.1016/J.Jmb.2009.12.052 |
0.589 |
|
2009 |
Sgourakis NG, Garcia AE. Modeling and Simulation Of A Protein Tertiary Complex: Study of the Interaction Interface and Conformational Dynamics of Dark State Rhodopsin in complex with Transducin Biophysical Journal. 96: 368a-369a. DOI: 10.1016/J.Bpj.2008.12.1985 |
0.572 |
|
2008 |
Sgourakis NG, Day R, McCallum SA, Garcia AE. Pressure effects on the ensemble dynamics of ubiquitin inspected with molecular dynamics simulations and isotropic reorientational eigenmode dynamics. Biophysical Journal. 95: 3943-55. PMID 18621814 DOI: 10.1529/Biophysj.108.133702 |
0.532 |
|
2007 |
Sgourakis NG, Yan Y, McCallum SA, Wang C, Garcia AE. The Alzheimer's peptides Abeta40 and 42 adopt distinct conformations in water: a combined MD / NMR study. Journal of Molecular Biology. 368: 1448-57. PMID 17397862 DOI: 10.1016/J.Jmb.2007.02.093 |
0.52 |
|
2005 |
Sgourakis NG, Bagos PG, Papasaikas PK, Hamodrakas SJ. A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models. Bmc Bioinformatics. 6: 104. PMID 15847681 DOI: 10.1186/1471-2105-6-104 |
0.324 |
|
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