Shohei Koide - Publications

Affiliations: 
Biochemistry and Molecular Biology University of Chicago, Chicago, IL 
Area:
Biochemistry, Molecular Biology

109 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Zorba A, Nguyen V, Koide A, Hoemberger M, Zheng Y, Kutter S, Kim C, Koide S, Kern D. Allosteric modulation of a human protein kinase with monobodies. Proceedings of the National Academy of Sciences of the United States of America. PMID 31239342 DOI: 10.1073/pnas.1906024116  0.48
2018 Gupta A, Xu J, Lee S, Tsai ST, Zhou B, Kurosawa K, Werner MS, Koide A, Ruthenburg AJ, Dou Y, Koide S. Facile target validation in an animal model with intracellularly expressed monobodies. Nature Chemical Biology. PMID 30013062 DOI: 10.1038/s41589-018-0099-z  0.48
2018 Last NB, Stockbridge RB, Wilson AE, Shane T, Kolmakova-Partensky L, Koide A, Koide S, Miller C. A CLC-type F/H antiporter in ion-swapped conformations. Nature Structural & Molecular Biology. PMID 29941917 DOI: 10.1038/s41594-018-0082-0  0.48
2018 Tanaka SI, Takahashi T, Koide A, Iwamoto R, Koikeda S, Koide S. Monobody-mediated alteration of lipase substrate specificity. Acs Chemical Biology. PMID 29757606 DOI: 10.1021/acschembio.8b00384  0.48
2018 Zhang Z, Liang WG, Bailey LJ, Tan YZ, Wei H, Wang A, Farcasanu M, Woods VA, McCord LA, Lee D, Shang W, Deprez-Poulain R, Deprez B, Liu DR, Koide A, ... Koide S, et al. Ensemble cryoEM elucidates the mechanism of insulin capture and degradation by human insulin degrading enzyme. Elife. 7. PMID 29596046 DOI: 10.7554/eLife.33572  0.48
2018 Diver MM, Pedi L, Koide A, Koide S, Long SB. Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT. Nature. PMID 29342140 DOI: 10.1038/nature25439  0.48
2017 Reckel S, Gehin C, Tardivon D, Georgeon S, Kükenshöner T, Löhr F, Koide A, Buchner L, Panjkovich A, Reynaud A, Pinho S, Gerig B, Svergun D, Pojer F, Güntert P, ... ... Koide S, et al. Structural and functional dissection of the DH and PH domains of oncogenic Bcr-Abl tyrosine kinase. Nature Communications. 8: 2101. PMID 29235475 DOI: 10.1038/s41467-017-02313-6  0.48
2017 Ghosh E, Srivastava A, Baidya M, Kumari P, Dwivedi H, Nidhi K, Ranjan R, Dogra S, Koide A, Yadav PN, Sidhu SS, Koide S, Shukla AK. A synthetic intrabody-based selective and generic inhibitor of GPCR endocytosis. Nature Nanotechnology. PMID 28967893 DOI: 10.1038/nnano.2017.188  0.48
2017 Salzman GS, Zhang S, Gupta A, Koide A, Koide S, Araç D. Stachel-independent modulation of GPR56/ADGRG1 signaling by synthetic ligands directed to its extracellular region. Proceedings of the National Academy of Sciences of the United States of America. PMID 28874577 DOI: 10.1073/pnas.1708810114  0.48
2017 Spencer-Smith R, Li L, Prasad S, Koide A, Koide S, O'Bryan JP. Targeting the α4-α5 interface of RAS results in multiple levels of inhibition. Small Gtpases. 0. PMID 28692342 DOI: 10.1080/21541248.2017.1333188  0.48
2017 Rizk SS, Mukherjee S, Koide A, Koide S, Kossiakoff AA. Targeted rescue of cancer-associated IDH1 mutant activity using an engineered synthetic antibody. Scientific Reports. 7: 556. PMID 28373671 DOI: 10.1038/s41598-017-00728-1  0.48
2017 Kükenshöner T, Schmit NE, Bouda E, Sha F, Pojer F, Koide A, Seeliger M, Koide S, Hantschel O. Selective Targeting of SH2 Domain-Phosphotyrosine Interactions of Src Family Tyrosine Kinases with Monobodies. Journal of Molecular Biology. PMID 28347651 DOI: 10.1016/j.jmb.2017.03.023  0.48
2017 Bowman A, Koide A, Goodman JS, Colling ME, Zinne D, Koide S, Ladurner AG. sNASP and ASF1A function through both competitive and compatible modes of histone binding. Nucleic Acids Research. 45: 643-656. PMID 28123037 DOI: 10.1093/nar/gkw892  0.48
2016 Spencer-Smith R, Koide A, Zhou Y, Eguchi RR, Sha F, Gajwani P, Santana D, Gupta A, Jacobs M, Herrero-Garcia E, Cobbert J, Lavoie H, Smith M, Rajakulendran T, Dowdell E, ... ... Koide S, et al. Inhibition of RAS function through targeting an allosteric regulatory site. Nature Chemical Biology. PMID 27820802 DOI: 10.1038/nchembio.2231  0.48
2016 Sachleben JR, Adhikari AN, Gawlak G, Hoey RJ, Liu G, Joachimiak A, Montelione GT, Sosnick TR, Koide S. Aromatic Claw: A new fold with high aromatic content that evades structural prediction. Protein Science : a Publication of the Protein Society. PMID 27750371 DOI: 10.1002/pro.3069  0.48
2016 Salzman GS, Ackerman SD, Ding C, Koide A, Leon K, Luo R, Stoveken HM, Fernandez CG, Tall GG, Piao X, Monk KR, Koide S, Araç D. Structural Basis for Regulation of GPR56/ADGRG1 by Its Alternatively Spliced Extracellular Domains. Neuron. 91: 1292-1304. PMID 27657451 DOI: 10.1016/j.neuron.2016.08.022  1
2016 Shao Y, Huang H, Qin D, Li NS, Koide A, Staley JP, Koide S, Kossiakoff AA, Piccirilli JA. Specific Recognition of a Single-stranded RNA Sequence by a Synthetic Antibody Fragment. Journal of Molecular Biology. PMID 27593161 DOI: 10.1016/j.jmb.2016.08.029  1
2016 Wojcik J, Lamontanara AJ, Grabe G, Koide A, Akin L, Gerig B, Hantschel O, Koide S. Allosteric Inhibition of Bcr-Abl Kinase by High-Affinity Monobody Inhibitors Directed to the SH2-Kinase Interface. The Journal of Biological Chemistry. PMID 26912659 DOI: 10.1074/jbc.M115.707901  0.48
2016 Hattori T, Lai D, Dementieva IS, Montaño SP, Kurosawa K, Zheng Y, Akin LR, Świst-Rosowska KM, Grzybowski AT, Koide A, Krajewski K, Strahl BD, Kelleher NL, Ruthenburg AJ, Koide S. Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation. Proceedings of the National Academy of Sciences of the United States of America. PMID 26862167 DOI: 10.1073/pnas.1522691113  1
2015 Nady N, Gupta A, Ma Z, Swigut T, Koide A, Koide S, Wysocka J. ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation. Elife. 4. PMID 26523391 DOI: 10.7554/eLife.10150  1
2015 Zhong N, Loppnau P, Seitova A, Ravichandran M, Fenner M, Jain H, Bhattacharya A, Hutchinson A, Paduch M, Lu V, Olszewski M, Kossiakoff AA, Dowdell E, Koide A, Koide S, et al. Optimizing Production of Antigens and Fabs in the Context of Generating Recombinant Antibodies to Human Proteins. Plos One. 10: e0139695. PMID 26437229 DOI: 10.1371/journal.pone.0139695  0.48
2015 Stockbridge RB, Kolmakova-Partensky L, Shane T, Koide A, Koide S, Miller C, Newstead S. Crystal structures of a double-barrelled fluoride ion channel. Nature. PMID 26344196 DOI: 10.1038/nature14981  0.48
2015 Tanaka S, Takahashi T, Koide A, Ishihara S, Koikeda S, Koide S. Monobody-mediated alteration of enzyme specificity. Nature Chemical Biology. 11: 762-4. PMID 26322825 DOI: 10.1038/nchembio.1896  0.48
2015 Stuwe T, Bley CJ, Thierbach K, Petrovic S, Schilbach S, Mayo DJ, Perriches T, Rundlet EJ, Jeon YE, Collins LN, Huber FM, Lin DH, Paduch M, Koide A, Lu V, ... ... Koide S, et al. Architecture of the fungal nuclear pore inner ring complex. Science (New York, N.Y.). PMID 26316600 DOI: 10.1126/science.aac9176  0.48
2015 Hornsby M, Paduch M, Miersch S, Sääf A, Matsuguchi T, Lee B, Wypisniak K, Doak A, King D, Usatyuk S, Perry K, Lu V, Thomas W, Luke J, Goodman J, ... ... Koide S, et al. A High Through-put Platform for Recombinant Antibodies to Folded Proteins. Molecular & Cellular Proteomics : McP. PMID 26290498 DOI: 10.1074/mcp.O115.052209  0.48
2014 Zhang X, Hoey R, Koide A, Dolios G, Paduch M, Nguyen P, Wu X, Li Y, Wagner SL, Wang R, Koide S, Sisodia SS. A synthetic antibody fragment targeting nicastrin affects assembly and trafficking of γ-secretase. The Journal of Biological Chemistry. 289: 34851-61. PMID 25352592 DOI: 10.1074/jbc.M114.609636  1
2014 Stockbridge RB, Koide A, Miller C, Koide S. Proof of dual-topology architecture of Fluc F- channels with monobody blockers. Nature Communications. 5: 5120. PMID 25290819 DOI: 10.1038/ncomms6120  1
2014 Koide S, Kortemme T. Editorial overview: Engineering and design: raising the bar through innovation and integration. Current Opinion in Structural Biology. 27: vi-viii. PMID 25175941 DOI: 10.1016/j.sbi.2014.08.004  1
2014 Shukla AK, Westfield GH, Xiao K, Reis RI, Huang LY, Tripathi-Shukla P, Qian J, Li S, Blanc A, Oleskie AN, Dosey AM, Su M, Liang CR, Gu LL, Shan JM, ... ... Koide S, et al. Visualization of arrestin recruitment by a G-protein-coupled receptor. Nature. 512: 218-22. PMID 25043026 DOI: 10.1038/nature13430  1
2014 Yasui N, Findlay GM, Gish GD, Hsiung MS, Huang J, Tucholska M, Taylor L, Smith L, Boldridge WC, Koide A, Pawson T, Koide S. Directed network wiring identifies a key protein interaction in embryonic stem cell differentiation. Molecular Cell. 54: 1034-41. PMID 24910098 DOI: 10.1016/j.molcel.2014.05.002  0.48
2013 Sha F, Gencer EB, Georgeon S, Koide A, Yasui N, Koide S, Hantschel O. Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains. Proceedings of the National Academy of Sciences of the United States of America. 110: 14924-9. PMID 23980151 DOI: 10.1073/pnas.1303640110  1
2013 Hattori T, Taft JM, Swist KM, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Krajewski K, Strahl BD, White KP, Farnham PJ, Zhao Y, Koide S. Recombinant antibodies to histone post-translational modifications. Nature Methods. 10: 992-5. PMID 23955773 DOI: 10.1038/nmeth.2605  1
2013 McCord LA, Liang WG, Dowdell E, Kalas V, Hoey RJ, Koide A, Koide S, Tang WJ. Conformational states and recognition of amyloidogenic peptides of human insulin-degrading enzyme. Proceedings of the National Academy of Sciences of the United States of America. 110: 13827-32. PMID 23922390 DOI: 10.1073/pnas.1304575110  0.48
2013 Shukla AK, Manglik A, Kruse AC, Xiao K, Reis RI, Tseng WC, Staus DP, Hilger D, Uysal S, Huang LY, Paduch M, Tripathi-Shukla P, Koide A, Koide S, Weis WI, et al. Structure of active β-arrestin-1 bound to a G-protein-coupled receptor phosphopeptide. Nature. 497: 137-41. PMID 23604254 DOI: 10.1038/nature12120  1
2013 Koide S, Huang J. Generation of high-performance binding proteins for peptide motifs by affinity clamping. Methods in Enzymology. 523: 285-302. PMID 23422435 DOI: 10.1016/B978-0-12-394292-0.00013-8  1
2013 Lu M, Symersky J, Radchenko M, Koide A, Guo Y, Nie R, Koide S. Structures of a Na+-coupled, substrate-bound MATE multidrug transporter. Proceedings of the National Academy of Sciences of the United States of America. 110: 2099-104. PMID 23341609 DOI: 10.1073/pnas.1219901110  0.48
2013 Paduch M, Koide A, Uysal S, Rizk SS, Koide S, Kossiakoff AA. Generating conformation-specific synthetic antibodies to trap proteins in selected functional states. Methods (San Diego, Calif.). 60: 3-14. PMID 23280336 DOI: 10.1016/j.ymeth.2012.12.010  1
2013 Persson H, Ye W, Wernimont A, Adams JJ, Koide A, Koide S, Lam R, Sidhu SS. CDR-H3 diversity is not required for antigen recognition by synthetic antibodies. Journal of Molecular Biology. 425: 803-11. PMID 23219464 DOI: 10.1016/j.jmb.2012.11.037  1
2012 Nishikori S, Hattori T, Fuchs SM, Yasui N, Wojcik J, Koide A, Strahl BD, Koide S. Broad ranges of affinity and specificity of anti-histone antibodies revealed by a quantitative peptide immunoprecipitation assay. Journal of Molecular Biology. 424: 391-9. PMID 23041298 DOI: 10.1016/j.jmb.2012.09.022  1
2012 Miller KR, Koide A, Leung B, Fitzsimmons J, Yoder B, Yuan H, Jay M, Sidhu SS, Koide S, Collins EJ. T cell receptor-like recognition of tumor in vivo by synthetic antibody fragment. Plos One. 7: e43746. PMID 22916301 DOI: 10.1371/journal.pone.0043746  1
2012 Koide A, Koide S. Affinity maturation of single-domain antibodies by yeast surface display. Methods in Molecular Biology (Clifton, N.J.). 911: 431-43. PMID 22886267 DOI: 10.1007/978-1-61779-968-6_26  1
2012 Gilbreth RN, Koide S. Structural insights for engineering binding proteins based on non-antibody scaffolds. Current Opinion in Structural Biology. 22: 413-20. PMID 22749196 DOI: 10.1016/j.sbi.2012.06.001  1
2012 Zhang X, Hoey RJ, Lin G, Koide A, Leung B, Ahn K, Dolios G, Paduch M, Ikeuchi T, Wang R, Li YM, Koide S, Sisodia SS. Identification of a tetratricopeptide repeat-like domain in the nicastrin subunit of γ-secretase using synthetic antibodies. Proceedings of the National Academy of Sciences of the United States of America. 109: 8534-9. PMID 22586122 DOI: 10.1073/pnas.1202691109  1
2012 Kitahara R, Simorellis AK, Hata K, Maeno A, Yokoyama S, Koide S, Akasaka K. A delicate interplay of structure, dynamics, and thermodynamics for function: a high pressure NMR study of outer surface protein A. Biophysical Journal. 102: 916-26. PMID 22385863 DOI: 10.1016/j.bpj.2011.12.010  1
2012 Koide S, Koide A, Lipovšek D. Target-binding proteins based on the 10th human fibronectin type III domain (¹⁰Fn3). Methods in Enzymology. 503: 135-56. PMID 22230568 DOI: 10.1016/B978-0-12-396962-0.00006-9  1
2012 Koide A, Wojcik J, Gilbreth RN, Hoey RJ, Koide S. Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold. Journal of Molecular Biology. 415: 393-405. PMID 22198408 DOI: 10.1016/j.jmb.2011.12.019  1
2011 Grebien F, Hantschel O, Wojcik J, Kaupe I, Kovacic B, Wyrzucki AM, Gish GD, Cerny-Reiterer S, Koide A, Beug H, Pawson T, Valent P, Koide S, Superti-Furga G. Targeting the SH2-kinase interface in Bcr-Abl inhibits leukemogenesis. Cell. 147: 306-19. PMID 22000011 DOI: 10.1016/j.cell.2011.08.046  0.48
2011 Uysal S, Cuello LG, Cortes DM, Koide S, Kossiakoff AA, Perozo E. Mechanism of activation gating in the full-length KcsA K+ channel. Proceedings of the National Academy of Sciences of the United States of America. 108: 11896-9. PMID 21730186 DOI: 10.1073/pnas.1105112108  1
2011 Gilbreth RN, Truong K, Madu I, Koide A, Wojcik JB, Li NS, Piccirilli JA, Chen Y, Koide S. Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design. Proceedings of the National Academy of Sciences of the United States of America. 108: 7751-6. PMID 21518904 DOI: 10.1073/pnas.1102294108  1
2011 Koldobskaya Y, Duguid EM, Shechner DM, Suslov NB, Ye J, Sidhu SS, Bartel DP, Koide S, Kossiakoff AA, Piccirilli JA. A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination. Nature Structural & Molecular Biology. 18: 100-6. PMID 21151117 DOI: 10.1038/nsmb.1945  1
2010 Shemon AN, Heil GL, Granovsky AE, Clark MM, McElheny D, Chimon A, Rosner MR, Koide S. Characterization of the Raf kinase inhibitory protein (RKIP) binding pocket: NMR-based screening identifies small-molecule ligands. Plos One. 5: e10479. PMID 20463977 DOI: 10.1371/journal.pone.0010479  1
2010 Biancalana M, Koide S. Molecular mechanism of Thioflavin-T binding to amyloid fibrils. Biochimica Et Biophysica Acta. 1804: 1405-12. PMID 20399286 DOI: 10.1016/j.bbapap.2010.04.001  1
2010 Wojcik J, Hantschel O, Grebien F, Kaupe I, Bennett KL, Barkinge J, Jones RB, Koide A, Superti-Furga G, Koide S. A potent and highly specific FN3 monobody inhibitor of the Abl SH2 domain. Nature Structural & Molecular Biology. 17: 519-27. PMID 20357770 DOI: 10.1038/nsmb.1793  1
2010 Huang J, Koide S. Rational conversion of affinity reagents into label-free sensors for Peptide motifs by designed allostery. Acs Chemical Biology. 5: 273-7. PMID 20143785 DOI: 10.1021/cb900284c  1
2009 Takacs Z, Toups M, Kollewe A, Johnson E, Cuello LG, Driessens G, Biancalana M, Koide A, Ponte CG, Perozo E, Gajewski TF, Suarez-Kurtz G, Koide S, Goldstein SA. A designer ligand specific for Kv1.3 channels from a scorpion neurotoxin-based library. Proceedings of the National Academy of Sciences of the United States of America. 106: 22211-6. PMID 20007782 DOI: 10.1073/pnas.0910123106  1
2009 Huang J, Nagy SS, Koide A, Rock RS, Koide S. A peptide tag system for facile purification and single-molecule immobilization. Biochemistry. 48: 11834-6. PMID 19928925 DOI: 10.1021/bi901756n  1
2009 Wu C, Biancalana M, Koide S, Shea JE. Binding modes of thioflavin-T to the single-layer beta-sheet of the peptide self-assembly mimics. Journal of Molecular Biology. 394: 627-33. PMID 19799914 DOI: 10.1016/j.jmb.2009.09.056  1
2009 Koide A, Wojcik J, Gilbreth RN, Reichel A, Piehler J, Koide S. Accelerating phage-display library selection by reversible and site-specific biotinylation. Protein Engineering, Design & Selection : Peds. 22: 685-90. PMID 19737805 DOI: 10.1093/protein/gzp053  1
2009 Koide S. Generation of new protein functions by nonhomologous combinations and rearrangements of domains and modules. Current Opinion in Biotechnology. 20: 398-404. PMID 19700302 DOI: 10.1016/j.copbio.2009.07.007  1
2009 Huang J, Makabe K, Biancalana M, Koide A, Koide S. Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution. Journal of Molecular Biology. 392: 1221-31. PMID 19646997 DOI: 10.1016/j.jmb.2009.07.067  0.48
2009 Koide S. Engineering of recombinant crystallization chaperones. Current Opinion in Structural Biology. 19: 449-57. PMID 19477632 DOI: 10.1016/j.sbi.2009.04.008  1
2009 Uysal S, Vásquez V, Tereshko V, Esaki K, Fellouse FA, Sidhu SS, Koide S, Perozo E, Kossiakoff A. Crystal structure of full-length KcsA in its closed conformation. Proceedings of the National Academy of Sciences of the United States of America. 106: 6644-9. PMID 19346472 DOI: 10.1073/pnas.0810663106  1
2009 Koide S, Sidhu SS. The importance of being tyrosine: lessons in molecular recognition from minimalist synthetic binding proteins. Acs Chemical Biology. 4: 325-34. PMID 19298050 DOI: 10.1021/cb800314v  1
2009 Granovsky AE, Clark MC, McElheny D, Heil G, Hong J, Liu X, Kim Y, Joachimiak G, Joachimiak A, Koide S, Rosner MR. Raf kinase inhibitory protein function is regulated via a flexible pocket and novel phosphorylation-dependent mechanism. Molecular and Cellular Biology. 29: 1306-20. PMID 19103740 DOI: 10.1128/MCB.01271-08  1
2009 Biancalana M, Makabe K, Koide A, Koide S. Molecular mechanism of thioflavin-T binding to the surface of beta-rich peptide self-assemblies. Journal of Molecular Biology. 385: 1052-63. PMID 19038267 DOI: 10.1016/j.jmb.2008.11.006  1
2008 Makabe K, Koide S. The promiscuity of beta-strand pairing allows for rational design of beta-sheet face inversion. Journal of the American Chemical Society. 130: 14370-1. PMID 18842042 DOI: 10.1021/ja805011h  1
2008 Biancalana M, Makabe K, Koide A, Koide S. Aromatic cross-strand ladders control the structure and stability of beta-rich peptide self-assembly mimics. Journal of Molecular Biology. 383: 205-13. PMID 18762191 DOI: 10.1016/j.jmb.2008.08.031  1
2008 Dutta S, Koide A, Koide S. High-throughput analysis of the protein sequence-stability landscape using a quantitative yeast surface two-hybrid system and fragment reconstitution. Journal of Molecular Biology. 382: 721-33. PMID 18674545 DOI: 10.1016/j.jmb.2008.07.036  1
2008 Kossiakoff AA, Koide S. Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces. Current Opinion in Structural Biology. 18: 499-506. PMID 18638552 DOI: 10.1016/j.sbi.2008.06.004  1
2008 Gilbreth RN, Esaki K, Koide A, Sidhu SS, Koide S. A dominant conformational role for amino acid diversity in minimalist protein-protein interfaces. Journal of Molecular Biology. 381: 407-18. PMID 18602117 DOI: 10.1016/j.jmb.2008.06.014  1
2008 Huang J, Koide A, Makabe K, Koide S. Design of protein function leaps by directed domain interface evolution. Proceedings of the National Academy of Sciences of the United States of America. 105: 6578-83. PMID 18445649 DOI: 10.1073/pnas.0801097105  1
2008 Tereshko V, Uysal S, Koide A, Margalef K, Koide S, Kossiakoff AA. Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold. Protein Science : a Publication of the Protein Society. 17: 1175-87. PMID 18445622 DOI: 10.1110/ps.034892.108  1
2008 Makabe K, Biancalana M, Yan S, Tereshko V, Gawlak G, Miller-Auer H, Meredith SC, Koide S. High-resolution structure of a self-assembly-competent form of a hydrophobic peptide captured in a soluble beta-sheet scaffold. Journal of Molecular Biology. 378: 459-67. PMID 18367205 DOI: 10.1016/j.jmb.2008.02.051  0.36
2008 Ye JD, Tereshko V, Frederiksen JK, Koide A, Fellouse FA, Sidhu SS, Koide S, Kossiakoff AA, Piccirilli JA. Synthetic antibodies for specific recognition and crystallization of structured RNA. Proceedings of the National Academy of Sciences of the United States of America. 105: 82-7. PMID 18162543 DOI: 10.1073/pnas.0709082105  1
2008 Mallik B, Zhang L, Koide S, Morikis D. pH dependence of stability of the 10th human fibronectin type III domain: a computational study. Biotechnology Progress. 24: 48-55. PMID 17935345 DOI: 10.1021/bp0700915  1
2007 Makabe K, Yan S, Tereshko V, Gawlak G, Koide S. Beta-strand flipping and slipping triggered by turn replacement reveal the opportunistic nature of beta-strand pairing. Journal of the American Chemical Society. 129: 14661-9. PMID 17985889 DOI: 10.1021/ja074252c  0.36
2007 Koide A, Tereshko V, Uysal S, Margalef K, Kossiakoff AA, Koide S. Exploring the capacity of minimalist protein interfaces: interface energetics and affinity maturation to picomolar KD of a single-domain antibody with a flat paratope. Journal of Molecular Biology. 373: 941-53. PMID 17888451 DOI: 10.1016/j.jmb.2007.08.027  1
2007 Sidhu SS, Koide S. Phage display for engineering and analyzing protein interaction interfaces. Current Opinion in Structural Biology. 17: 481-7. PMID 17870470 DOI: 10.1016/j.sbi.2007.08.007  1
2007 Fellouse FA, Esaki K, Birtalan S, Raptis D, Cancasci VJ, Koide A, Jhurani P, Vasser M, Wiesmann C, Kossiakoff AA, Koide S, Sidhu SS. High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. Journal of Molecular Biology. 373: 924-40. PMID 17825836 DOI: 10.1016/j.jmb.2007.08.005  1
2007 Koide A, Gilbreth RN, Esaki K, Tereshko V, Koide S. High-affinity single-domain binding proteins with a binary-code interface. Proceedings of the National Academy of Sciences of the United States of America. 104: 6632-7. PMID 17420456 DOI: 10.1073/pnas.0700149104  1
2007 Yan S, Gawlak G, Makabe K, Tereshko V, Koide A, Koide S. Hydrophobic surface burial is the major stability determinant of a flat, single-layer beta-sheet. Journal of Molecular Biology. 368: 230-43. PMID 17335845 DOI: 10.1016/j.jmb.2007.02.003  0.48
2007 Koide A, Zhao C, Naganuma M, Abrams J, Deighton-Collins S, Skafar DF, Koide S. Identification of regions within the F domain of the human estrogen receptor alpha that are important for modulating transactivation and protein-protein interactions. Molecular Endocrinology (Baltimore, Md.). 21: 829-42. PMID 17185393 DOI: 10.1210/me.2006-0203  0.48
2007 Koide A, Koide S. Monobodies: antibody mimics based on the scaffold of the fibronectin type III domain. Methods in Molecular Biology (Clifton, N.J.). 352: 95-109. PMID 17041261 DOI: 10.1385/1-59745-187-8:95  1
2006 Makabe K, McElheny D, Tereshko V, Hilyard A, Gawlak G, Yan S, Koide A, Koide S. Atomic structures of peptide self-assembly mimics. Proceedings of the National Academy of Sciences of the United States of America. 103: 17753-8. PMID 17093048 DOI: 10.1073/pnas.0606690103  0.48
2006 Makabe K, Tereshko V, Gawlak G, Yan S, Koide S. Atomic-resolution crystal structure of Borrelia burgdorferi outer surface protein A via surface engineering. Protein Science : a Publication of the Protein Society. 15: 1907-14. PMID 16823038 DOI: 10.1110/ps.062246706  0.36
2006 Clark MC, McElheny D, Wojcik J, Kurutz J, Rosner MR, Koide S. NMR assignment of rat Raf kinase inhibitor protein. Journal of Biomolecular Nmr. 36: 4. PMID 16456706 DOI: 10.1007/s10858-005-4424-y  0.48
2006 Skafar DF, Koide S. Understanding the human estrogen receptor-alpha using targeted mutagenesis. Molecular and Cellular Endocrinology. 246: 83-90. PMID 16442702 DOI: 10.1016/j.mce.2005.12.015  1
2006 Huang J, Koide A, Nettle KW, Greene GL, Koide S. Conformation-specific affinity purification of proteins using engineered binding proteins: Application to the estrogen receptor Protein Expression and Purification. 47: 348-354. PMID 16325424 DOI: 10.1016/j.pep.2005.10.021  1
2005 Dutta S, Batori V, Koide A, Koide S. High-affinity fragment complementation of a fibronectin type III domain and its application to stability enhancement. Protein Science : a Publication of the Protein Society. 14: 2838-48. PMID 16199661 DOI: 10.1110/ps.051603005  1
2005 Jha AK, Colubri A, Zaman MH, Koide S, Sosnick TR, Freed KF. Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. Biochemistry. 44: 9691-702. PMID 16008354 DOI: 10.1021/bi0474822  1
2004 Murphy WL, Mercurius KO, Koide S, Mrksich M. Substrates for Cell Adhesion Prepared via Active Site-Directed Immobilization of a Protein Domain Langmuir. 20: 1026-1030. PMID 15803670 DOI: 10.1021/la035733m  1
2004 Karatan E, Merguerian M, Han Z, Scholle MD, Koide S, Kay BK. Molecular recognition properties of FN3 monobodies that bind the Src SH3 domain. Chemistry & Biology. 11: 835-44. PMID 15217616 DOI: 10.1016/j.chembiol.2004.04.009  1
2004 Yan S, Gawlak G, Smith J, Silver L, Koide A, Koide S. Conformational heterogeneity of an equilibrium folding intermediate quantified and mapped by scanning mutagenesis. Journal of Molecular Biology. 338: 811-25. PMID 15099747 DOI: 10.1016/j.jmb.2004.02.063  0.48
2003 Hertadi R, Gruswitz F, Silver L, Koide A, Koide S, Arakawa H, Ikai A. Unfolding mechanics of multiple OspA substructures investigated with single molecule force spectroscopy. Journal of Molecular Biology. 333: 993-1002. PMID 14583195 DOI: 10.1016/j.jmb.2003.09.010  1
2003 Zhao C, Koide A, Abrams J, Deighton-Collins S, Martinez A, Schwartz JA, Koide S, Skafar DF. Mutation of Leu-536 in human estrogen receptor-alpha alters the coupling between ligand binding, transcription activation, and receptor conformation. The Journal of Biological Chemistry. 278: 27278-86. PMID 12736255 DOI: 10.1074/jbc.M303840200  1
2003 Richards J, Miller M, Abend J, Koide A, Koide S, Dewhurst S. Engineered fibronectin type III domain with a RGDWXE sequence binds with enhanced affinity and specificity to human alphavbeta3 integrin. Journal of Molecular Biology. 326: 1475-88. PMID 12595259 DOI: 10.1016/S0022-2836(03)00082-2  1
2002 Batori V, Koide A, Koide S. Exploring the potential of the monobody scaffold: effects of loop elongation on the stability of a fibronectin type III domain. Protein Engineering. 15: 1015-20. PMID 12601141  1
2002 Pawley NH, Koide S, Nicholson LK. Backbone dynamics and thermodynamics of Borrelia outer surface protein A. Journal of Molecular Biology. 324: 991-1002. PMID 12470954 DOI: 10.1016/S0022-2836(02)01146-4  1
2002 Nakagawa T, Shimizu H, Link K, Koide A, Koide S, Tamura A. Calorimetric dissection of thermal unfolding of OspA, a predominantly beta-sheet protein containing a single-layer beta-sheet. Journal of Molecular Biology. 323: 751-62. PMID 12419262  0.48
2002 Yan S, Kennedy SD, Koide S. Thermodynamic and kinetic exploration of the energy landscape of Borrelia burgdorferi OspA by native-state hydrogen exchange. Journal of Molecular Biology. 323: 363-75. PMID 12381326 DOI: 10.1016/S0022-2836(02)00882-3  1
2002 Koide A, Abbatiello S, Rothgery L, Koide S. Probing protein conformational changes in living cells by using designer binding proteins: Application to the estrogen receptor Proceedings of the National Academy of Sciences of the United States of America. 99: 1253-1258. PMID 11818562 DOI: 10.1073/pnas.032665299  1
2001 Ohnishi S, Koide A, Koide S. The roles of turn formation and cross-strand interactions in fibrillization of peptides derived from the OspA single-layer β-sheet Protein Science. 10: 2083-2092. PMID 11567099 DOI: 10.1110/ps.15901  1
2001 Yudt MR, Koide S. Preventing estrogen receptor action with dimer-interface peptides Steroids. 66: 549-558. PMID 11322963 DOI: 10.1016/S0039-128X(00)00224-5  1
2000 Ohnishi S, Koide S. Proteins without a hydrophobic core: structure and stability Tanpakushitsu Kakusan Koso. Protein, Nucleic Acid, Enzyme. 45: 2502-2510. PMID 11086410  1
2000 Ohnishi S, Koide A, Koide S. Solution conformation and amyloid-like fibril formation of a polar peptide derived from a β-hairpin in the OspA single-layer β-sheet Journal of Molecular Biology. 301: 477-489. PMID 10926522 DOI: 10.1006/jmbi.2000.3980  1
1998 Koide A, Bailey CW, Huang X, Koide S. The fibronectin type III domain as a scaffold for novel binding proteins Journal of Molecular Biology. 284: 1141-1151. PMID 9837732 DOI: 10.1006/jmbi.1998.2238  1
1998 Pham TN, Koide S. NMR studies of Borrelia burgdorferi OspA, a 28 kDa protein containing a single-layer β-sheet Journal of Biomolecular Nmr. 11: 407-414. PMID 9691284  1
1998 Pham TN, Koide A, Koide S. A stable single-layer β-sheet without a hydrophobic core Nature Structural Biology. 5: 115-119. PMID 9461076 DOI: 10.1038/nsb0298-115  1
1997 Koide S, Bailev CW, Koide A. Directed evolution of fibronectin type iii domain to novel ligand binding proteins Faseb Journal. 11.  1
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